This study was conducted to clarify the characteristics of small-scale enterprises (SSEs) with fewer than 50 workers, which employ 62.2% of all Japanese workers. Subjects were 71,183 workers employed at 1,761 workplaces in Tochigi, Japan, in 2002. Frequencies of abnormal lifestyle and health check-up data were described according to the category of the enterprise. Adjusted odds ratios (ORs) of the abnormal findings were calculated by logistic regression analysis. Dose-response relationships were calculated by trend tests. The frequency of abnormal findings was higher in SSEs than in other categories of enterprises. The ORs of work intensity, alcohol consumption, current smoker, and the Brinkmann index were higher in SSEs than in large-scale enterprises (LSEs) and were also significant in trend tests. The ORs of audiometry, hypertension, glucose in urine and ECG in males and females, BMI, liver function, lipid metabolism, and blood sugar in females, chest X-ray, and anemia in males were higher in SSEs. Audiometry, hypertension, anemia, ECG in both males and females; chest X-ray, and glucose in urine in males, and liver function, lipid metabolism and blood sugar in females showed significant results in trend tests. Overall health and healthy lifestyle in SSEs were worse than in LSEs.