Rapid eye movement sleep in males is characterized by penile erection along with EEG desynchronization, muscle atonia, ponto-geniculo-occipital waves, and rapid eye movements (REM). The central neural mechanisms regulating sleep related erections (SREs) are not known. Recently, the lateral preoptic area has been shown to contribute in sleep-related erectile mechanisms. The present study was conducted to examine the involvement of the septum for these SREs. Experiments were carried out in adult male Wistar rats (180-250 g) and electrodes were implanted for recording sleep parameters i.e. EEG, EMG and EOG under sodium pentobarbital anesthesia. Bulbospongiosus (BS) muscle EMG was recorded for monitoring penile activity. All the recording electrodes were connected to an IC socket, and the whole assembly was fixed to the skull with dental cement. After post-operative recovery, all the parameters were recorded for 24 hrs. The medial and lateral septi were bilaterally lesioned using NMDA (5 µg/ 0.2 µl), in two different sets of rats, and recordings were taken on days 6 and 15 after the lesion. At the completion of the experiments, the lesion sites were verified histologically. Lesion at the lateral septum produced a significant decrease in the BS muscle activity during REM as compared to pre-lesion control. The rat with lesion in the medial septum showed increase in the REM associated BS muscle activity after the lesion. These findings suggest that the septum plays important role in REM sleep related penile erection.