INTRODUCTION Demographic changes in Japan have resulted in an increased number of elderly living alone. AIM The aim of this study was to identify if there is an association between frailty and living alone. METHODS We conducted a cross-sectional study of 1602 Japanese men and women living in isolated islands. Information obtained included height, body weight, handgrip strength, and family structure; antihypertensive, hypoglycaemic, and lipid-lowering medication use; history of stroke or ischaemic heart disease, smoking history, alcohol intake, joint pain or swelling. Relevant laboratory test results were obtained from recent health check-ups. The Frailty Index for Japanese elderly, a 15-item self-report questionnaire was completed by participants and the Kessler Psychological Distress Scale (K6) was administered. RESULTS After individuals aged below 60 years old or those with missing data were excluded, data from 1224 participants were analysed. Living alone (single household family structure) was significantly associated with frailty in men (odds ratio [OR] 3.85; 95% confidence interval [CI] 1.94-7.65), but not in women (OR 1.08; 95% CI 0.72-1.63). This association in men remained statistically significant after adjustment for known risk factors for frailty. DISCUSSION In the elderly population in rural Nagasaki, men living alone have a high risk of frailty. Screening and intervention to prevent frailty in this population is urgently needed.