Crystal violet is used as a textile and paper dye, and is a component of navy blue and black inks for printing, ball-point pens, and inkjet printers. It is sometimes used to colourize diverse products such as fertilizer, antifreeze, detergent, and leather.
The dye is used as a histological stain, particularly in Gram staining for classifying bacteria.
When conducting DNA gel electrophoresis, crystal violet can be used as a nontoxic DNA stain as an alternative to fluorescent, intercalating dyes such as ethidium bromide. Used in this manner, it may be either incorporated into the agarose gel or applied after the electrophoresis process is finished. Used at a 0.001% concentration and allowed to stain a gel after electrophoresis for 30 minutes, it can detect as little as 16 ng of DNA. Through use of a methyl orange counterstain and a more complex staining method, sensitivity can be improved further to 8 ng of DNA. When crystal violet is used as an alternative to fluorescent stains, it is not necessary to use ultraviolet illumination; this has made crystal violet popular as a means of avoiding UV-induced DNA destruction when performing DNA cloning in vitro.
In biomedical research, crystal violet can be used to stain the nuclei of adherent cells. In this application, crystal violet works as an intercalating dye and allows the quantification of DNA which is proportional to the number of cells.
In forensics, crystal violet was used to develop fingerprints. Crystal violet is also used as a tissue stain in the preparation of light microscopy sections. In laboratory, solutions containing crystal violet and formalin are often used to simultaneously fix and stain cells grown in tissue culture to preserve them and make them easily visible, since most cells are colourless. It is also sometimes used as a cheap way to put identification markings on laboratory mice; since many strains of lab mice are albino, the purple colour stays on their fur for several weeks.
In body piercing, gentian violet is commonly used to mark the location for placing piercings, including surface piercings.
Marking blue, used to mark out pieces in metalworking, is composed of methylated spirits, shellac, and gentian violet.