The enzyme and binding protein dipeptidyl peptidase IV (DPPIV/CD26) has a unique enzymatic specificity in cleaving dipeptides from neuropeptides, chemokines, and hormones. Thus, DPPIV is potentially involved in the regulation of functions of the immune, endocrine, and nervous systems. In the present study, we compared DPPIV-deficient, mutant Japanese [F344/DuCrj(DPPIV-)] and German [F344/Crl(Ger/DPPIV-)] F344 rat substrains with a wild-type-like F344 substrain [F344/Crl(Por)] from the United States in a multitiered strategy using a number of different behavioral tests. General health, neurological and motor functions, and sensory abilities of the different F344 substrains were not different. A reduced body weight and a reduced water consumption were observed in mutant animals. DPPIV-deficient rats exhibited increased pain sensitivity in a non-habituated hot plate test, indicative of a reduced stress-induced analgesia. In line with this finding, reduced stress-like responses in tasks like the open field (OF), social interaction (SI), and passive avoidance test were found. Differences in DPPIV-like activity appear to be involved in neurophysiological processes because DPPIV-deficient animals were less susceptible to the sedative effects of ethanol. The varying phenotypes of the F344 substrains are likely to be mediated by differential degradation of DPPIV substrates such as substance P, glucagon-like peptide (GLP)-1, enterostatin, and especially neuropeptide Y (NPY). Potentially, DPPIV-deficient substrains represent an important tool for biomedical research, focusing on the involvement of DPPIV and its substrates in behavioral and physiological processes.