High-intensity interval training (HIIT) has recently received much attention as a new option for aerobic training. Despite its smaller time requirement, HIIT has been reported to have a greater effect than continuous moderate-intensity training on fat loss, especially a decrease in truncal adiposity. We therefore examined whether long-term HIIT preferentially modulates truncal adiposity rather than peripheral adiposity, especially thigh adiposity, where local muscle energy consumption increased profoundly during HIIT. We also examined the association between changes in adipose tissue distribution and serum adiponectin level. Twelve healthy male participants (28-48 years old) were assigned to a group that performed HIIT using only a leg ergometer (L-HIIT, n = 7) or to a group that performed HIIT using both leg and arm ergometers (LA-HIIT, n = 5) twice weekly for 16 weeks. The training programs consisted of 8 to 12 sets of >90% V ・ O 2 peak for 1 min, with 1 min of very light active recovery. Body composition analyses as well as aerobic fitness and measurements of serum adiponectin were performed at baseline and after intervention. A linear improvement in aerobic fitness was observed along with a decrease in leg fat (5.4 ± 1.7 vs. 5.1 ± 1.7 kg, p < 0.05) near the main working muscles during HIIT in the combined (L+LA-HIIT) group. Moreover, there was an association of decrease in leg fat or thigh adiposity with improvement in aerobic fitness in the combined group (ρ = -0.59, p < 0.05; and ρ = -0.71, p < 0.05, respectively). Visceral adiposity was decreased in L-HIIT (115 ± 45 vs. 100 ± 47 cm 2 , p < 0.05), however no decrease was observed in total fat or truncal fat in either group. No change was observed in serum adiponectin concentration in either group. Changes in serum adiponectin were associated with changes in visceral adiposity in the combined group (ρ = -0.72, p < 0.01). Regional rather than whole-body fat loss was observed after a 16-week HIIT program.