It has been shown that the medial hypothalamus exerts facilitatory control over female sexual behavior in the rat whereas the septal area exerts inhibitory control over lordosis behavior. The present study assessed whether the septal area exerts its inhibitory control over lordosis behavior via efferent connections with the mediobasal hypothalamus. Anatomical studies using retrograde tracers verified that cell bodies located in the lateral septal area project ipsilaterally to the mediobasal hypothalamus. Based upon the predominantly ipsilateral connection between the lateral septum and mediobasal hypothalamus, unilateral frontolateral knife cuts were produced on the left or right side of the mediobasal hypothalamus or else sham surgeries. Subsequently all animals were given unilateral electrolytic septal lesions on the right side of the brain. These animals had septal damage that was located either ipsilateral or contralateral with respect to the knife cuts. Female sexual behavior was tested following the hypothalamic knife cuts and retested after unilateral septal lesions. Unilateral hypothalamic knife cuts on either side of the brain had no detectable effect on female sexual behavior when compared to the sham group. However, following unilateral septal lesions a significant increase in lordosis behavior was observed in all groups following treatment with estrogen alone. There were no differences in lordosis behavior between the groups which had septal lesions located ipsilateral vs. contralateral with respect to the hypothalamic knife cuts. These results support the hypothesis that the facilitation in lordosis behavior associated with electrolytic septal lesions is not mediated by neural connections between the septal area and mediobasal hypothalamus. These two brain areas thus appear to exert separate and independent control over female sexual behavior.