Interspecies Protocol was a semester-long course at Starfleet Academy examining the rules, regulations, and customs for interaction between alien species and Starfleet personnel.

Kathryn Janeway reminded Harry Kim of the class, and his participation in it, when he became involved with Derran Tal. (VOY: "The Disease")

The context of this conversation indicated that Interspecies Protocol dealt with issues of interspecific reproduction. The reasoning behind it is exampled in the Varro and the Bolians, two species known to cause sexual complications for Humans.