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Small-scale enterprises (SSEs) usually share poorer resources for promoting occupational health.To investigate inequality of health status among SSEs in Japan.A cross-sectional, multiple-centred study was carried out using the periodical health check-up data for the fiscal year 2000 to compare the age-adjusted proportions of workers with hypertension (HT), hyperlipidaemia, impaired glucose tolerance (IGT) and obesity and of current smokers by size of enterprise, i.e. ≤29, 30–49, 50–99, 100–299, 300–999 and ≥1000 employees in Japan.From five leading occupational health organizations, data were collected for 9833 enterprises with a total of 436 729 subjects, 302 383 males and 134 346 females. The proportions of workers in SSEs with ≤49 employees with HT, IGT and obesity were 8.5, 5.0 and 3.5%, respectively, higher than those in enterprises with ≥50 male employees. The prevalence of smokers in SSEs with ≤49 employees was 61%, 2–6% higher than in enterprises with ≥50 male employees. These proportions showed a significantly increasing tendency with decreasing size of male workforce.Despite the cross-sectional design and only adjusting age as a potential confounder, higher proportions of HT, IGT, obesity and smoking in male workers were found in SSEs compared to larger organizations.