A Paper Chromatography Experiment Kids Can Run Today

Black is not a colour in a marker. It is a recipe. Put a dot of washable black marker on a strip of coffee filter, stand the strip in a centimetre of water, and over about fifteen minutes the dot climbs upward and falls apart into pink, blue and yellow bands in a fixed order. This paper chromatography experiment kids can run with nothing but a jar and a marker is also, in simplified form, the method a forensic lab uses to tell two pens apart and a doping lab uses to find a banned substance in urine. The order of the bands is not random, and by the end of this you will be able to explain exactly what sets it.

Key Takeaways

• You dot a marker on filter paper, let water climb through it, and the single ink mark separates into its component dyes, which you then measure as Rf values.
• Use washable markers with water. A permanent marker will barely move, and that failure is worth showing on purpose.
• Black, brown and green separate most dramatically. Yellow usually does not separate at all, which is itself a result.
• Best for ages 6 to 12, with the quantitative Rf version from about age 10.
• What usually goes wrong: the water level starts above the ink dot, which washes the dye straight off into the jar.

What You’ll Need

Item	How much	Where to get it	If you don’t have it
Washable felt-tip markers	4–6 colours, including black	Any stationery shop; Crayola Washable and similar	Food colouring diluted 1 drop in 5 drops of water, applied with a toothpick
Paper coffee filters	2–3	Supermarket	Lab filter paper, or a white paper towel with no embossed pattern. Printer paper will not work
Clear glass jar or tumbler	1 per strip	Kitchen	A short drinking glass. It needs to be shorter than your strip
Tap water	About 1 cm depth per jar	n/a	Distilled water gives marginally cleaner bands
Pencil	1	n/a	Must be pencil. Pen ink on the baseline will run and ruin the strip
Ruler marked in mm	1	n/a	n/a
Clothes pegs or paper clips	1 per strip	n/a	Tape the strip to a pencil laid across the jar mouth
Scissors	1	n/a	Adult cuts the strips for under-8s
70% isopropyl or rubbing alcohol	30 mL, optional	Pharmacy	Only for the permanent-marker variation, and only handled by an adult. Flammable, keep away from flames, irritating to eyes

Time: prep 10 min, experiment 20 min, cleanup 5 min Cost: everything is probably in your kitchen, except possibly the coffee filters Mess level: low, though washable marker on a white worktop still needs a cloth

Do the Experiment: A Paper Chromatography Experiment Kids Can Run

Step 1 - Cut strips and draw a pencil baseline

Cut the coffee filter into strips about 2 cm wide and 10 cm long. Flatten the curve as best you can. With a pencil, draw a light line across each strip 1.5 cm from one end. That line is your baseline, and every measurement later is taken from it.

Step 2 - Load a concentrated spot

Put a single dot of marker on the baseline, in the middle of the strip. Wait fifteen seconds for it to dry, then dot the same place again. Three layers makes a spot dense enough to give clear bands. Keep the dot small, 3 mm or less; a fat blob smears into a stripe and the bands overlap.

Step 3 - Set up the jar with the water below the line

Pour tap water into the jar to a depth of about 1 cm. Hang the strip so its bottom edge dips into the water but the pencil line and the ink dot stay above the water surface. Clip the top of the strip to a pencil laid across the mouth of the jar. Getting this wrong is the single most common failure.

Step 4 - Ask for a prediction, then wait

Ask: “The dot is black. When the water climbs through it, what colours will come out, and which one will end up highest?” Record the guess. Then leave it alone. Do not jog the jar.

What you should see: Water creeps up the paper by capillary action at about 1 cm per minute at first, slowing as it rises. Within two minutes the black dot starts to smear and a pink or magenta halo appears. By five to eight minutes you should see distinct bands. Black washable marker typically gives magenta lowest, then cyan or blue, then a yellow band running near the front, sometimes with a grey-brown smudge left at the baseline.

Step 5 - Stop it before the front reaches the top

When the wet front is about 1 cm from the top of the strip, lift the strip out and immediately mark the position of the front with a pencil. The front is invisible once the paper dries, and if you forget this you cannot calculate anything.

Step 6 - Lay the strip flat, dry it, and measure

Dry it on a plate for ten minutes. Then measure, in millimetres from the baseline, the distance to the centre of each coloured band, and the distance to the solvent front. Calculate Rf for each band: Rf = distance travelled by the band ÷ distance travelled by the front. Every Rf value will be between 0 and 1.

Step 7 - Run a comparison and a failure

Set up two more strips: one with a different brand of black marker, and one with a permanent marker in water.

What you should see: Different brands of black give different Rf sets, which is the point of the forensic version. The permanent marker barely leaves the baseline, because its dyes are not water-soluble. That is not a failed run; it is the control that shows the solvent matters as much as the ink.

What’s Actually Going On

Chromatography separates a mixture by making its components race through a medium at different speeds. There are two phases. The stationary phase is the paper: cellulose fibres with a thin layer of water bound tightly to their surface. The mobile phase is the water climbing the strip by capillary action, pulled by the attraction between water and cellulose and held together by its own surface tension.

Each dye molecule in the ink is constantly swapping between the two. For a fraction of the time it sits adsorbed on the wet cellulose, going nowhere; for the rest it is dissolved in the moving water and travelling. A dye that spends more of its time dissolved in the mobile phase travels further. A dye that binds strongly to cellulose lags behind. The Rf value, the ratio of band distance to front distance, is a number that expresses that balance, and for a given paper and solvent it is roughly reproducible, which is what makes it useful for identification rather than just decoration.

This is why the explanation you usually hear is wrong. “The lighter colours travel further” is not a mechanism at all; colour has nothing to do with it. “Smaller molecules move faster” is closer but still misleading, since molecular size is only one of the things affecting how strongly a dye sticks. The real driver is relative affinity: how much the molecule prefers water over cellulose, which depends on its charge, its polarity and its hydrogen-bonding groups. A sulfonated azo dye with charged groups is very water-soluble and shoots to the front. A larger, flatter, less polar pigment hugs the paper.

The method is not a kitchen curiosity. Archer Martin and Richard Synge published the partition theory behind it in the Biochemical Journal in 1941 and shared the 1952 Nobel Prize in Chemistry for it. Every modern analytical technique with “chromatography” in its name, including the gas chromatography-mass spectrometry that screens athletes and the liquid chromatography that checks drug purity, runs on the same partition idea with a different stationary phase and a pump.

One more honest detail. The dyes in your marker are not secret. Writing inks commonly use a small set of synthetic dyes, several of them related to the colour additives the US Food and Drug Administration regulates and lists by number. When the yellow band runs almost to the solvent front, you are watching a specific, named, mass-produced molecule behave the way its chemistry dictates.

How to Explain It to Your Kid

Ages 5–8: The colours are running a race and some get stuck

Tell them the paper is sticky to some colours and slippery to others. The water is a bus going up the paper, and every colour keeps hopping on and off. Colours that like the bus ride further; colours that like the paper get left behind. Have them point at the highest band and say which colour likes the water best. Let them run three or four markers side by side and predict each one. Green is a satisfying one to start with because the blue and yellow come apart cleanly.

Ages 9–12: Rf is a number that identifies a dye

Introduce the word chromatography and the Rf calculation. Have them measure their own strip in millimetres and compute two or three Rf values on paper. Then make it a puzzle: run three black markers unlabelled, record the Rf sets, and see whether they can match a mystery dot to the right pen. That is a real forensic procedure, and it works. The same idea of combining a few ingredients to make a colour appears from the other direction in why paint mixing and light mixing disagree.

Ages 13+: Change the solvent and explain the shift

Run the same black marker with three mobile phases: tap water, a 1% salt solution (1 g salt in 100 mL water), and 70% isopropyl alcohol under adult handling. The Rf values move, and in a direction you can reason about: more polar dyes travel further in more polar solvents. Ask them to predict the direction before each run and to explain the result in terms of the dye’s affinity for each phase. Then look up thin-layer chromatography and ask what changes when the stationary phase becomes silica instead of cellulose.

The question to ask: “If I gave you a mystery purple dot and the strips from six different markers, how would you work out which pen made it, and what would convince you that you were right rather than lucky?”

Why Teaching This Early Pays Off

Separating mixtures is one of the first genuinely useful ideas in chemistry, and it arrives in most curricula somewhere between ages 10 and 13 alongside filtration, distillation and evaporation. Children who have only met it on a worksheet tend to collapse all four into “getting things out of other things.” Children who have watched a single black dot resolve into three bands have a concrete case where the separation depends on a property they can name, which makes the whole family of methods easier to tell apart later.

It also trains measurement from a ratio, which is quietly valuable. Rf is dimensionless. It does not care whether your strip was 8 cm or 12 cm, as long as you measure both distances the same way. Ratios that cancel out the apparatus are everywhere in science, and meeting one at age ten in a context this tangible is a good deal.

The research caution is the same one that applies to every experiment in this series. Chi and Wylie’s ICAP framework, published in 2014, ranks interactive and constructive engagement above merely active participation, which here means the explaining and the predicting carry the learning, not the pouring. Doing the activity in silence is close to watching it. Asking for a prediction before Step 4, and asking for an explanation after Step 7, is what turns twenty minutes into something that lasts.

Before You Start: What Parents Should Know

Best age	6 to 12. A six-year-old can do the whole water version; Rf calculations suit 10 and up
Supervision	Close for under-8s only because of the scissors. The water version needs no chemical supervision at all
Real hazards	None with washable markers and water. The optional alcohol variation uses 70% isopropyl, which is flammable and irritates eyes; an adult should pour it, use it away from any flame or hob, and work with a window open
Don’t	Don’t use alcohol in a sealed jar left to stand, and don’t substitute nail-polish remover, paint thinner or methylated spirits for isopropyl. Acetone dissolves some plastics and gives worse separation anyway

When It Doesn’t Work

• The dot washes off into the water. The water level started above the baseline. Pour some out so the surface sits at least 1 cm below the pencil line, and reload a fresh strip.
• One grey smear, no bands. Either the marker is permanent, or the spot was too big. Redo with a 3 mm dot of a washable marker. If you want permanent-marker separation, you need alcohol, not water.
• The front races up and stalls halfway. Usually printer paper or glossy paper rather than filter paper. Printer paper is sized with a coating that blocks capillary flow. Use a coffee filter or a plain paper towel.
• The bands run diagonally or the front is crooked. The strip is touching the side of the jar, or the strip is curved. Keep it hanging free and flatten the filter first.
• Nothing separates even with washable black. Some black markers use a single pigment dispersion rather than a dye blend. Try another brand. Brown and green are the most reliable starting colours if you need a result on the first attempt.

Take It Further

• Make it forensic. Label four black pens A to D on the bottom of the jars only, run all four, record the Rf sets, then have someone else make a mystery dot. Match it. Then discuss what would happen if two brands shared a dye supplier, which is a real limitation of the technique.
• Plot Rf against solvent. Run the same marker in water, 1% salt solution, and 50% and 70% isopropyl alcohol, and tabulate Rf for each band. The trend across four solvents is a proper data set and a genuinely original science-fair entry, because almost nobody varies the mobile phase.
• Separate something from the kitchen. Spinach leaf crushed in a little isopropyl alcohol gives a green spot that separates into chlorophyll a, chlorophyll b and carotenoids, which is how plant pigments were first studied. Use the same strips and a longer run. This pairs well with our wider guide to safe kitchen chemistry experiments and extends the simpler version in paper chromatography and the science of colour.

What to Watch For Over the Next 3 Months

• Week 4: They notice that a spilled drink on a napkin spreads its colours unevenly, and say so. That is the same physics, unprompted.
• Month 2: The word “dissolve” starts appearing with a qualifier: dissolves in water, dissolves in alcohol. That distinction is the whole foundation of “like dissolves like.”
• Month 3: If they ask how a lab can tell how much of something is in a sample rather than just what is in it, they have found the gap between qualitative and quantitative analysis. That question is worth taking seriously and is the doorway to instrumental chemistry.

Frequently Asked Questions

Why does my black marker not separate at all?

Most likely it is permanent. Permanent-marker dyes are dissolved in alcohol-based solvents and are not water-soluble, so water cannot carry them. Run it with 70% isopropyl alcohol instead, with an adult handling the alcohol, and it will separate.

Can I use paper towel instead of coffee filters?

Yes, as long as it is plain white with no embossed pattern and no printed design. The embossing channels the water and skews the front. Coffee filters are more uniform and give straighter bands, which matters if you want to measure Rf.

Why does the yellow band end up on top?

Because the yellow dyes in common inks are small, heavily sulfonated and extremely water-soluble, so they spend most of their time in the moving water rather than stuck to the paper. It is about solubility, not about yellow being “lighter.”

How accurate are Rf values at home?

Good enough to tell two pens apart, not good enough for publication. Expect repeatability within about 0.05 across runs if you keep the same paper, the same water and the same run length. Temperature, humidity and how long you let it run all shift the numbers.

Is it safe for a five-year-old to drink from the jar afterwards?

No. Nothing in this experiment is food-grade once the ink has run into the water, even with washable markers. Wash the jars normally and treat the run-off as paint water, not a drink.

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About the author

Ricky Flores is the founder of HiWave Makers and an electrical engineer with 15+ years of experience building consumer technology at Apple, Samsung, and Texas Instruments. He writes about how kids learn to build, think, and create in a tech-saturated world. Read more at hiwavemakers.com.

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Sources

1. Martin, A. J. P., & Synge, R. L. M. (1941). “A new form of chromatogram employing two liquid phases.” Biochemical Journal, 35(12), 1358–1368. https://doi.org/10.1042/bj0351358
2. The Nobel Foundation. “The Nobel Prize in Chemistry 1952: Archer John Porter Martin and Richard Laurence Millington Synge.” https://www.nobelprize.org/prizes/chemistry/1952/summary/
3. US Food and Drug Administration. “Color Additives History.” https://www.fda.gov/industry/color-additives/color-additives-history
4. Chi, M. T. H., & Wylie, R. (2014). “The ICAP Framework: Linking Cognitive Engagement to Active Learning Outcomes.” Educational Psychologist, 49(4), 219–243. https://doi.org/10.1080/00461520.2014.965823
5. Alfieri, L., Brooks, P. J., Aldrich, N. J., & Tenenbaum, H. R. (2011). “Does discovery-based instruction enhance learning?” Journal of Educational Psychology, 103(1), 1–18. https://doi.org/10.1037/a0021017
6. National Research Council. (2012). A Framework for K-12 Science Education. National Academies Press. https://doi.org/10.17226/13165