[3] In biosciences, it is used as a vital stain to selectively colour dead tissues or cells blue.

Trypan blue is so-called because it can kill trypanosomes, the parasites that cause sleeping sickness.

An analog of trypan blue, suramin, is used pharmacologically against trypanosomiasis.

Trypan blue is commonly used in microscopy (for cell counting) and in laboratory mice for assessment of tissue viability.

Trypan blue is also used in ophthalmic cataract surgery to stain the anterior capsule in the presence of a mature cataract, to aid in visualization, before creating the continuous curvilinear capsulorhexis.