Eye specialists say they could be putting children's eyesight under strain and pupils could be struggling even to see what has been written on the board.
That much-loved red is apparently the worst offender. Why? Because there is not enough contrast between the board and the pen colour.
Kevin Lewis, president-elect of the British college of optometry, said: "Reds are a nightmare. A whiteboard is a source of glare; it can be very bright, especially on sunny days when there is a window casting extra light on it. Bright background glare washes out the eye, making it hard to pick up details.
"The problem with red especially is that it has very low contrast and the eye is not that sensitive to it."
Pastels also cause trouble for children. "Teachers may think using lots of colour helps to get children interested in what's on the board but it can actually cause them to struggle to see," said Mr Lewis. "We would recommend using black, and if you want colours, use dark greens and blues."
As far as eyesight goes, old-fashioned blackboards were clear winners, according to Mr Lewis. "We see white on black better, and blackboards had that dark background which the eye prefers. Visually impaired people often have to switch their computer screens to a dark background so they can pick out the letters more easily."
Steve Ryan, an optician at Chalmers and Sons, in Roath, Cardiff, said the problem has increased as whiteboards have replaced blackboards.
"When a child comes in complaining of not being able to read the board properly, my first question is always 'What colour does the teacher use?'
Invariably, it's a lot of red. It really makes it harder to see the detail.
And some children, mostly boys, can also be red-green colour defective, so using a coloured pen will only add to their problems."
He advises children to ask their teachers to use black or dark pens.