It is used in histology for staining collagen;[2] for that purpose it is a standard dye in North America.

It is a component of Papanicolaou stains together with eosin Y and bismarck brown Y.

When fading is to be avoided, it is replaced with fast green FCF, which also has more brilliant color.

Lissamine green dye can be used to check the health of the anterior surfaces of the eye.

It is available on a swab, which is wet with saline and then the dye is dropped into the lower fornix.