Acoustic startle response and its plasticity, e.g., habituation and prepulse inhibition (PPI), have been extensively investigated, being altered in several neuropsychiatric disorders. Yet, little is known about the expression of startle-related behaviors during adolescence, a critical phase in the development of a variety of major neuropsychiatric pathologies. The present study investigated for the first time startle behaviors across adolescence in male mice of the inbred strains C57BL/6J and DBA/2J. Pre-pubertal (4 weeks of age) mice displayed reduced startle reactivity and altered PPI compared to adult animals (8 weeks of age), but these effects were observed only in the C57BL/6J strain. Strain differences were also clearly detected for startle response, habituation, and PPI. All effects were modulated by the intensity of the pulse stimulus and were not confounded by differences in anxiety levels. Our data demonstrate that genetic factors and the early adolescent phase are critically important considerations in the design of mouse models of neuropsychiatric disturbances.