This study aimed to examine the cross-sectional association of non-standard employment with cardiovascular disease risk factors. Five yr of data from the Comprehensive Survey of Living Conditions and National Health and Nutritional Survey were combined. We used logistic regression to examine the association of employment contract (non-standard [part-time, dispatched, or contract] vs. standard [full-time and permanent]) with eight cardiovascular disease risk factors among 1,636 men and 2,067 women aged 40–60 yr. There were significant associations between non-standard employment and cardiovascular disease risk factors such as current smoking among men (odds ratio [OR] 1.39; 95% confidential interval [CI], 1.13–1.86) and diabetes among women (OR 1.83; 95% CI, 1.10–3.09). Non-standard employment was associated with a few cardiovascular disease risk factors in this middle-aged cohort in Japan.