Aim To clarify the performance situation of selected quality indicators: falls, pressure ulcers and dehydration, at health care facilities for the elderly in Japan, and what structural characteristics are related to them. Methods The operational population consisted of 1057 institutionalized users (approximately 10 randomly selected per facility) from a survey answered by the care staff. The facilities were divided into two groups according to their prevalence of negative outcomes (falls, pressure ulcers, dehydration): the best 25% (the very good performers) and the remaining 75% (not so good performers). Logistic regression analysis was carried out to examine the relationship between the structure characteristics of the facilities and their performance regarding each quality indicator. Results After controlling for sex, years of operation and average age of the users, our results showed a beneficial significant relationship between falls and the total number of nurses per 100 users with an adjusted odds ratio (AOR) of 0.77 (95% CI 0.59–0.98); In contrast, for pressure ulcers, harmful associations between a higher number of registered nurses (AOR 1.23, 95% CI 1.01–1.05) and the availability of 24‐h nurse staffing (AOR 4.95, 95% CI 1.19–24.91) were found; regarding dehydration, we did not find any related staffing characteristics. Conclusion Nursing staff might be considered as a potentially related variable in the quality of care in health care facilities for the elderly. The present study is the first to show a relationship between structural characteristics and quality outcomes in health care facilities for the elderly. Geriatr Gerontol Int 2013; 14: 301–308.