Adiponectin is reduced in obesity and has been suggested to play an important role in modulation of atherosclerosis. We studied the relationship between visceral (VAT) and subcutaneous (SAT) adipose tissue and serum adiponectin concentrations in Japanese men. Participants were 304 randomly selected community-based Japanese men aged 40-49 without a prior history of cardiovascular disease. Participants were grouped according to tertiles of serum adiponectin. In multiple linear regression analysis including age, pack years of smoking, and alcohol intake as covariates, log-transformed adiponectin was inversely associated with both VAT and SAT when these two obesity measures were included separately in the models. However, log-transformed adiponectin was inversely associated with VAT (standardized beta estimate=-0.465; P<0.0001) and positively associated with SAT (standardized beta estimate=1.277; P=0.03), when these were included concomitantly in the model. In conclusion, VAT and SAT had differential associations with serum adiponectin concentrations.