Previous studies have demonstrated that meeting the dietary recommendations for macronutrients was significantly associated with higher cardiorespiratory fitness (CRF) levels in adults. However, the relation between the status of micronutrient intake and CRF still remains unclear. This study examined the association between micronutrient intake status (based on adherence to the dietary reference intakes (DRI)) and CRF in Japanese men. The study comprised 373 Japanese men aged 30–69 years. Dietary intake was assessed with a self-administered diet history questionnaire. Overall micronutrient intake status was quantified using an overall nutrient adequacy score (ONAS) for thirteen selected micronutrients. ONAS was calculated based on adherence to the DRI for Japanese. CRF was defined as O2max during a maximal incremental test on a bicycle ergometer. Physical activity was measured using accelerometer-based activity monitors for seven consecutive days. We observed a significant inverse trend for the prevalence of inadequacy for the intake of vitamin A and Ca across incremental CRF categories (P < 0·05). In a multivariate model, the ONAS was positively associated with absolute (β = 0·10, P = 0·02) and relative O2max (β = 0·09, P = 0·04), independent of physical activity. The OR for being unfit (the lowest 25 % of the age-specific distribution of O2max) in the third ONAS tertile compared with the first ONAS tertile was 0·52 (95 % CI 0·28, 0·96). These results demonstrated that the intake of several individual micronutrients and overall micronutrient intake status are independently and positively associated with CRF in Japanese men.