Adipose tissue distribution is an important predictor of obesity-associated morbidity and mortality. A central ('male') fat distribution is associated with increases in intra-abdominal adipose tissue which might be of metabolic importance. Although many recent studies have pointed out significant regional differences in the size and metabolism of subcutaneous fat cells intra-abdominal depots have not been systematically examined. We compared fat cell sizes (FCS) and lipoprotein lipase activity (LPLA) of two internal (omental, mesenteric) and four subcutaneous (SQ) sites (femoral, gluteal, abdominal, epigastric) in morbidly obese patients (26 premenopausal women and 14 men). Men had larger internal FCS than women while women had larger SQ FCS in the gluteal and femoral depots. Mesenteric FCS were largest of all sites in men. In women, omental fat cells were the smallest of all sites sampled but omental fat cells were as large as SQ sites in men. A more central distribution of fat in women (high waist/hip ratio) was associated with large mesenteric fat cells. Calculation of total fat cell number based on SQ FCS only, revealed sex differences that were eliminated by also using intra-abdominal FCS in the calculation. Averaged across all six sites, women had higher LPLA than men. Higher LPL activities were found in the lower-body subcutaneous sites with enlarged fat cells in women. However, the relative enlargement of intra-abdominal FCS in men was not associated with increased LPLA. In conclusion, sex- and site-specific variations in the distribution of FCS and LPLA in internal and SQ fat depots emphasize the importance of analyzing these depots in studies of fat cell number and adipose tissue metabolism.