The hypothalamus is a brain region of major importance in regulation of energy balance via autonomic nervous control of both intake and expenditure. There is substantial evidence that diets high in saturated fats lead to obesity while diets equally high in polyunsaturated fats (PUFAs) do not. Using c-Fos as a marker, this study aimed to investigate hypothalamic neuronal response in mice fed high fat diets (58% of calories as fat) emphasising saturated, n-3 or n-6 polyunsaturated fatty acids, or a low fat (10% of calories) diet over periods of 1 and 7 weeks. In addition, a 4-week "reversal" intervention with n-3 polyunsaturated or low fat diet was undertaken in saturated fat-fed mice. Food intake and body weight were measured over the feeding periods. At 1, 7 and 11 weeks mice were killed, epididymal fat pad were weighed and brains were removed for quantitation of hypothalamic c-Fos-like immunoreactive (FLI) neurons. Weight gain, and epididymal fat pad weight, were highest on the saturated fat diet and lowest on the n-3 diet despite similar food intakes (epididymal fat weight at week 7: saturated fat, 622+/-48 mg; n-6 fat 423+/-69; low fat 387+/-10, n-3 fat 225+/-26). Compared to a low fat diet, FLI neurons in the dorsal part of lateral hypothalamic (dLH) area was dramatically increased by saturated fat feeding (+367% at 1 week) while ventromedial hypothalamic (VMH) activity was decreased. In contrast with n-6 and n-3 feeding dLH FLI neuronal activity was unchanged but actually increased in the VMH. Paraventricular nucleus (PVN) FLI neurons increased in the high saturated group only at 7 and 11 weeks, after substantial fat accumulation. Substitution of saturated fat diet with the n-3 diet partially reversed (48%) the increase in FLI neurons in PVN of saturated fat-fed mice, while it significantly increase FLI neurons in arcuate nucleus (+400%). In summary, this study demonstrates that dietary saturated fat modulates hypothalamic neuronal activity in a pattern (high lateral, reduced ventromedial activity) consistent with its obesogenic effects. In contrast, diets equally high in PUFA (particularly of the n-3 class) neither increase adiposity nor derange the lateral/medial neuronal activity balance.