The prefrontal cortex and the nucleus accumbens are two brain sites which are known to be involved in the modulation of the acoustic startle response. In particular, the release of monoaminergic transmitters within these brain sites plays an important role in prepulse inhibition of the startle response which serves as an operational measure of sensorimotor gating. Like for dopamine, it is well established that serotonin transmission plays an important role in prepulse inhibition. However, there are only few studies investigating the effects of local manipulation of serotonin transmission on prepulse inhibition. The aim of the present study was to test whether prepulse inhibition or the startle response itself was affected by serotonergic depletion of either the prefrontal cortex or the nucleus accumbens. Serotonergic depletion was induced by local injections of 5,7-dihydroxytryptamine and verified by ex vivo analysis of transmitter levels by high pressure liquid chromatography. In our behavioural tests, we found that 5,7-dihydroxytryptamine into the prefrontal cortex decreased prepulse inhibition, whereas injections into the nucleus accumbens facilitated prepulse inhibition. The time course of these behavioural effects, as well as the transmitter level changes within the different brain sites was very different. Most interestingly, 5,7-dihydroxytryptamine injections into the nucleus accumbens affect serotonin and dopamine levels in both, nucleus accumbens and prefrontal cortex. Taken together, the present study supports an important role of serotonin in the modulation of prepulse inhibition and baseline startle magnitude. However, the observed changes cannot be attributed to a specific brain site since our data clearly show that local 5,7-dihydroxytryptamine injections also affect transmitter levels in brain sites away from the injection site.