Chromatography with coloured marker pens

Students separate the solution of colours in washable marker pen inks using chromatography. They can figure out what inks are used to make up a pack of markers. The dried pieces can be used to make art collages.
Science content
Chemistry: Physical Changes, Solutions, Mixtures and Separating (2, 4, 5, 6)
  • deep tubs e.g. yogurt tubs
  • water to fill tubs to a depth of about 1cm
  • white coffee filter papers (or paper towels work OK, but are not as vibrant)
  • tested cardboard templates (e.g. 11 X 2cm pieces of cereal box, with a line drawn across 2cm from one end)
  • scissors and pencils
  • coffee stirrer sticks
  • mini binder clips
  • water soluble pens of many colours (test before use)
  • paper towels

Please note that in a class of students it is likely that one of them is at least partially colourblind (1 in 12 males are colourblind). As this is an activity distinguishing colours, these students will not be able to tell some colours apart and perceive some colours differently, although the activity will be no less interesting for them. The common red/green colour blindness means reds and greens (or colours containing reds and greens such as browns) look similar. More information at and

Make a cardboard template of such a length so that when binder-clipped to the coffee stir stick it hangs to within 1cm of the bottom of the tub. Add a line across the template 2cm from the bottom. Add 1½ cm water to the tub.
Test the template and water level by cutting out a piece of filter paper the same size as the template, and drawing a marker line across, level with the line on the template. When clipped to the coffee stir stick the filter paper should just dip in the water, but the marker pen line does not. As the water creeps up the filter paper it draws up the colours of the marker.
Adjust the template if necessary, then make enough for the class.
Test out the markers available, to make sure that at least some of them are made up of two or more different colour inks.

Students use the template to cut out filter papers, add a marker line where indicated, as well as a dot of marker colour at the top of the filter paper strip (to remember what colour they started out with).
They can clip two or three filter paper strips to one stick, to run several chromatograms at a time, but should make sure that the filter papers do not touch each other or the sides of the tub.
Make sure they remove the strip from the water before the colours run into their coloured dot at the top, and lay it on a paper towel to dry.

Black, brown, blue, green colours usually work well. The darker colours are generally a mixture of more colours.
From a pack of marker pens, students can document what colour inks are in each pen, then figure out how many inks are used to make up a full pack of pens. They can record their results either on their own worksheet (attached), or better on a class table (see photos) that accumulates data as they all add to it.
Look at the data as a class, and question 'which marker pens are made of only one dye', which are made of many dyes' etc (see photo for discussion questions).

Extend with the activity Chromatography with the ink pens (black) for a forensics use of the method to identify the black pen that wrote a note.

By choosing the best colours to make chromatograms with, making wider sheets of filter paper to run multiple colours at once, then cutting and mounting the best patterns, some great art collages emerge (see photos).

The chemistry:
Chromatography is used for separating mixtures of molecules in a solution. This technique is used a lot by chemists and forensic scientists.
How does chromatography work?
The coloured dye molecules in the ink of the pen are attracted to both the water that it is in, but also the surface of the filter paper. Each different colour is attracted to the water or the filter paper to different extents. As the water moves up, the dye molecules that are most attracted to the water will move along fast with it. If the dye molecules are mostly attracted to the paper, they will get stuck to the paper and not move along with the water at all. Most colours are attracted to both the water and the paper, so will travel with the water for a while, then stick to the paper for a while. Depending on the relative attraction of a dye to the water and the paper, a colour will travel at its own rate. The differing rates of travel separate out the colours.


The youngest grades need assistance setting up, or work step by step all together for at least the first round. And to start, only give them brown and black markers, or they never try these less attractive colours (despite them being the most surprising and interesting mixture of colours).

Alternative method: students make dots of marker colour on filter paper pieces laid flat, then use the Q-tips to drip and smear drops of water over the colours to separate them.

Try the Exploratorium version:

The colour in children's markers is a dye - a solution of coloured molecules in water. Permanent markers, dry erase pens and ballpoint pens are also dyes in a solvent. Paints are generally a pigment - a colloid of solid particles suspended in a liquid. Pigment-based art materials are more opaque than dye-based art materials.
Should be able to see the difference between a dye and a pigment under the microscope.

Grades taught
Gr K
Gr 1
Gr 2
Gr 3
Gr 4
Gr 5
Gr 6
Gr 7