Widely ranging prevalence rates for metabolic syndrome (MetS) in patients taking clozapine have been reported on the basis of various criteria, and most studies have been carried out in non-Asian countries. Therefore, we examined the prevalence of MetS in Korean patients using three commonly applied criteria with two waist-circumference cutoff values. The indirectly standardized prevalence ratio (ISPR) was estimated using data from the Fourth Korean National Health and Nutrition Examination Survey (KNHNES, 2007) to compare the prevalence of MetS in patients with that in the general population. In addition, we also examined whether serum alanine aminotransferase (ALT) and aspartate aminotransferase levels serve as biochemical markers for the identification of MetS. We reviewed the electromedical records of patients with schizophrenia who had taken clozapine as the sole antipsychotic for 3 months or more. The prevalence of MetS ranged from 34.5 to 46.9%, and the ISPR ranged from 2.4 to 2.8, given the three definitions of MetS and the two waist-circumference cutoff points for women. The ISPR for MetS among those aged 18–30 years was the highest and decreased with age in both men and women. After adjusting for age, patients with normal serum ALT levels who were in the top third were significantly more likely to have MetS compared with those who were in the bottom third. Logistic regression analysis showed that serum ALT levels and use of antidepressants were significantly related to the presence of MetS. Korean patients with schizophrenia who were receiving clozapine as the sole antipsychotic showed a high prevalence of MetS. Although we found substantial differences in the prevalence according to criteria, the ISPR indicated significantly higher rates of MetS in this group than in the general population. In the general population, younger patients had a much higher risk for MetS than older patients. Elevated levels of serum ALT that were in the normal range were associated with the presence of MetS, which suggests the possibility of using serum ALT level as an early indicator for MetS in patients treated with clozapine.