We found previously that the ingestion of margarine containing medium-chain triacylglycerols (MCT) resulted in a significant increase in postprandial thermogenesis when compared with long-chain triacylglycerols (LCT). Diets that included margarine containing MCT and LCT were compared for 12 weeks in 73 subjects to investigate the effects on body weight, body fat, areas of subcutaneous and visceral fat, serum total cholesterols, triglycerides, lipoproteins, plasma glucose, serum insulin, total ketone bodies, and the activities of aspartate aminotransferase, alanine aminotransferase, and γ-glutamyltranspeptidase. We conducted a double-blind, controlled study and used blended rapeseed oil and soybean oil (LCT) as a comparison. Two groups ingested 2, 100−2, 400 kcal/day of energy, 65−73 g/day of total fat, and 14 g/day of test margarine (5 g/day of MCT or LCT). The subjects on the MCT diet demonstrated significant decreases in body fat weight (− 3.8 ± 2.4 kg vs − 2.4 ± 1.7 kg; MCT vs LCT, mean ± SD), subcutaneous fat (− 38.2 ± 29.9 cm2 vs − 22.6 ± 19.3 cm2), and visceral fat (− 12.2 ± 11.2 cm2 vs − 1.6 ± 12.8 cm2) after 12 weeks. There were no clinical differences in measured blood parameters. We suggest that the postprandial increase in thermogenesis and control of postprandial triglyceride levels may explain these results.