Relative to wildtype mice, mice lacking 5-HT1B receptors (5-HT1B KO) exhibit exaggerated heart rate and body temperature responses to environmental stimuli. In contrast, acoustic startle reactivity is reduced in 5-HT1B KO mice. We combined heart rate and temperature measurement with startle response paradigms in order to elucidate this apparent contradiction. Habituation and footshock-induced sensitization paradigms modulate startle reactivity. Reduced startle reactivity and unaltered habituation in 5-HT1B KO mice were replicated. Heart rate and temperature were unaffected by startle stimuli, but increased markedly in response to transportation and handling procedures. Footshocks caused a mild startle-sensitization and tachycardia in both genotypes. The physiological hyper-reactivity in 5-HT1B KO mice is a subtle phenotypic difference that contrasts with the phenotypic decrease in startle reactivity.