High dietary energy density (ED) has been associated with weight gain. However, little is known about the long-term effects of ED on weight changes among free-living subjects, particularly in Japanese and other Asian populations. In this study, we assessed dietary habits and weight changes in participants (5778 males and 7440 females, 35–69 years old) of the Takayama study. ED was estimated using a validated FFQ at baseline only. Information on body weight (BW) was obtained by self-administered questionnaires at baseline and follow-up. Mean BW difference in 9·8 years was 17 (se 4221) g for men and −210 (se 3889) g for women. In men, ED was positively associated with BW at follow-up after controlling for age, BW, height, physical activity score, alcohol consumption, energy intake, years of education at the baseline and change of smoking status during the follow-up. On average, men in the highest quartile of ED (>5·322 kJ/g (>1·272 kcal/g)) gained 138 (se 111) g, whereas men in the lowest ED (<1·057) lost 22 (se 111) g (Pfor trend=0·01). The association between ED and BW gain was stronger in men with normal weight. In women, the association between ED and weight change was not statistically significant. In conclusion, contrary to some studies that report an association between ED and weight gain in the overweight only, our data suggest that high-ED diets may be associated with weight gain in the lean population as well, at least in male subjects.