The septohippocampal system and the amygdala have been implicated in cognitive and emotional processes. A series of experiments was conducted to examine the effects of separate and combined lesions of these areas on a variety of behaviors, including: startle responses to acoustic stimuli; sensory gating, using prepulse inhibition of acoustic startle; anxiety, using the elevated plus-maze; locomotor activity in an open field; and memory, using both a spatial discrimination version of the Morris water maze and the inhibitory (passive) avoidance test. Both septal and fimbria-fornix lesions markedly impaired the acquisition of spatial information in the water maze, had anxiolytic-like effects in the elevated plus-maze, increased reactivity to footshock, and had marginal effects on prepulse inhibition and baseline startle. Septal and fimbria-fornix lesions also increased locomotor activity in the later stages of a session of open field exploration, but only septal lesions produced "freezing" during the early portion of this session and during inhibitory avoidance training. Amygdala lesions markedly impaired prepulse inhibition of acoustic startle. Amygdala lesions also attenuated the effects of septal lesions on freezing in the open field and on footshock reactivity, but did not affect the anxiolytic-like effects or hyperactivity associated with septal lesions. Amygdala lesions by themselves had no significant effect on water maze performance, but significantly potentiated the effects of septal lesions. These results suggest that there are dissociations between the effects of septal and fimbria-fornix lesions and that the interactions between the amygdala and septum in cognitive and emotional processes are task dependent.