This prospective study investigated the associations of various diet quality indices with mortality in Japan. Participants were 13 355 men and 15 724 women from the Takayama study. Eight diet quality indices were assessed using an FFQ: the Dietary Approaches to Stop Hypertension, alternative Mediterranean diet scores, Healthy Eating Index-2015, Alternate Healthy Eating Index-2010, Nutrient Rich Food Index 9.3, Diet Quality Score for Japanese, Japanese Food Guide Spinning Top and twelve-item Japanese Diet Index. Cox proportional models estimated hazard ratios and 95 % CI for all-cause and cause-specific mortality in a 1 sd difference for each index, with adjustment for confounders. During a mean follow-up of 14·1 years, 5339 deaths were recorded. Hazard ratios (95 % CI) per 1 sd higher index were 0·90 (0·87, 0·93) for Alternate Healthy Eating Index-2010, 0·92 (0·89, 0·95) for Diet Quality Score for Japanese, 0·93 (0·91, 0·96) for Nutrient Rich Food Index 9.3, 0·94 (0·92, 0·97) for alternative Mediterranean diet and Dietary Approaches to Stop Hypertension, 0·94 (0·91, 0·97) for Japanese Food Guide Spinning Top, 0·94 (0·91, 0·98) for twelve-item Japanese Diet Index and 0·97 (0·94, 0·996) for Healthy Eating Index-2015. Similar protective associations were observed for CVD mortality, but not for cancer mortality. These findings suggest that all eight indices are associated with lower mortality and that the strength of associations varies across indices; the Alternate Healthy Eating Index-2010 showed relatively strong associations, followed by the Diet Quality Score for Japanese, whereas the associations of the Healthy Eating Index-2015 appeared relatively weaker in this Japanese population.