The associations of dietary energy density with dietary intake and obesity have been largely unexplored in non-Western populations. The present cross-sectional study examined the associations using data from the 2012 National Health and Nutrition Survey, Japan. Dietary intake was assessed using a 1-d semi-weighed dietary record in 15 618 Japanese adults aged ≥20 years. Mean dietary energy density (calculated on the basis of foods only) was 5·98 (sd 1·20) kJ/g in men and 5·72 (sd 1·16) kJ/g in women. Dietary energy density was positively associated with intakes of bread, noodles (only men), meat, fats and oils, and sugar and confectionery but inversely with intakes of white rice (only men), potatoes, pulses, vegetables, fruits, and fish and shellfish. For nutrient intake, dietary energy density was positively associated with total fat and SFA but inversely associated with all other nutrients examined such as protein, carbohydrate, alcohol (only women), dietary fibre, and several vitamins and minerals, including Na. After adjustment for potential confounding factors, dietary energy density was positively associated with abdominal obesity (waist circumference ≥80 cm) in women (adjusted prevalence ratio between the extreme tertiles 1·07; 95 % CI 1·02, 1·12; Pfor trend=0·003). Dietary energy density was also positively but non-significantly associated with general obesity (BMI≥25 kg/m2) in women (Pfor trend=0·08). There were no such associations in men. In conclusion, lower energy density of the diets of Japanese adults was associated with favourable food and nutrient intake patterns, except for higher Na, and, in only women, a lower prevalence of abdominal obesity.