Previous studies on the relationship of local food environment with residents' diets have relied exclusively on self-reported information on diet, producing inconsistent results. Evaluation of dietary intake using biomarkers may obviate the biases inherent to the use of self-reported dietary information. This cross-sectional study examined the association between neighbourhood food store availability and 24 h urinary Na and K excretion. The subjects were 904 female Japanese dietetic students aged 18–22 years. Neighbourhood food store availability was defined as the number of food stores within a 0·5-mile (0·8-km) radius of residence. Urinary Na and K excretion and the ratio of urinary Na to K were estimated from a single 24 h urine sample. After adjustment for potential confounding factors, neighbourhood availability of confectionery stores/bakeries was inversely associated with urinary K, and was positively associated with the ratio of Na to K (P for trend = 0·008 and 0·03, respectively). Neighbourhood availability of rice stores showed an independent inverse association with urinary K (P for trend = 0·03), whereas neighbourhood availability of supermarkets/grocery stores conversely showed an independent positive association with this variable (P for trend = 0·03). Furthermore, neighbourhood availability of fruit/vegetable stores showed an independent inverse association with the ratio of Na to K (P for trend = 0·049). In a group of young Japanese women, increasing neighbourhood availability of supermarkets/grocery stores and fruit/vegetable stores and decreasing availability of confectionery stores/bakeries and rice stores were associated with favourable profiles of 24 h urinary K (and Na) excretion.