Evidence supports an association between metabolic syndrome (MetS) and schizophrenia. However, specific risk factors for MetS and gender differences in patients with schizophrenia taking second-generation antipsychotics (SGAs) have not been well explored. A cross-sectional cohort of 329 Han Chinese patients was recruited in a psychiatric hospital in central Taiwan. Using the definitions of the International Diabetes Federation for Chinese, the prevalence of MetS was 23.7 % (men: 25.7 %; women: 21.2 %). Logistic regression analyses showed that patients with a BMI ≥ 24 and an abnormal non-high-density lipoprotein cholesterol (non-HDL-C) were significantly ( p < 0.001) more likely to develop MetS. A BMI ≥ 24 was a significant risk factor in men (OR: 6.092, p < 0.001) and women (OR: 5.886, p < 0.001). An abnormal non-HDL-C was a significant specific risk factor for men with MetS (OR: 4.127, p < 0.001), but not for women. This study supports a greater prevalence of MetS in patients with schizophrenia taking SGAs than in the general population. Abnormal BMI and non-HDL-C were significantly associated with developing MetS, and an abnormal non-HDL-C was a specific risk factor for men. Future development of specific interventions and regular monitoring for MetS is imperative for early identification and prevention. [ABSTRACT FROM AUTHOR]