Women generally have a higher percentage of body fat than men. Also, women store more fat in the gluteal-femoral region, whereas men store more fat in the visceral (abdominal) depot. This review focuses on differences in regional fatty acid storage, mobilization and oxidation that may contribute to gender-related differences in body fat distribution. There are pronounced regional differences in the regulation of regional fatty acid metabolism between men and women. Firstly, there is evidence that in vivo, catecholamine mediated leg free fatty acid release is lower in women than in men, whereas free fatty acid release from the upper body depots is comparable. These data correspond to in-vitro adipose tissue biopsy data, which indicate a more pronounced difference in catecholamine mediated lipolysis between upper body and lower body fat depots in women than in men. Secondly, free fatty acid release by the upper body subcutaneous fat depots is higher in men than in women, indicating a higher resistance to the antilipolytic effect of meal ingestion in the upper body fat depots in men. Thirdly, there are indications that basal fat oxidation (adjusted for fat free mass) is lower in females as compared to males, thereby contributing to a higher fat storage in women. Finally, postprandial fat storage may be higher in subcutaneous adipose tissue in women than in men, whereas storage in visceral adipose tissue has been hypothesized to be higher in men. All the above differences may play a role in the variation in net regional fat storage between men and women, but the number of in-vivo studies on gender-related differences in fatty acid metabolism is very limited and most findings require confirmation. Furthermore, there is abundant evidence that the proportion of energy derived from fat during exercise is higher in women than in men. With respect to total body fat, this finding seems counterintuitive, as percentage body fat is increased in women. Further studies are necessary to investigate the significance of differences in exercise-induced fat oxidation on 24-h fat balance.