The increasing popularity of the mouse as a subject in basic science studies of pain can largely be attributed to the development of transgenic "knockout" technology in this species only. To take advantage of this biological technique, many investigators are rushing to adapt to the mouse experimental protocols that were designed for the rat. However, the myriad physiological and behavioral differences between these two rodent species render such adaptations non-trivial and in many cases seriously problematic. In this article we review the basic nociceptive assays used in behavioral pain research (thermal, mechanical, electrical and chemical), and highlight how species differences affect their proper application. In addition, some of the issues specifically pertaining to the interpretation of such data in knockout studies are addressed.