The Leica ST 4040 is equipped with one staining track with 27 stations including reagent and water stations. Five of these stations can be used for loading and five for unloading. Tap water station positions are selectable. To prevent loss of staining reagents through evaporation when not in operation, the staining track can be covered with the reagent lids provided.

As the instrument cover is divided into three sections, the user is protected from exposure to hazardous fumes by allowing the instrument to be open only in the zone being currently worked in. To further reduce exposure to hazardous reagent fumes, the Leica ST 4040 can be fitted with an activated carbon filter or a fume exhaust hose for direct venting to a fume hood. Two separate staining protocols can be programmed for quick operation, the program parameters being: staining time, draining time and agitation.