A modified version of the Waldrop scale (WS) was used to assess the prevalence of minor physical anomalies in schizophrenic patients (n = 71) and healthy controls (n = 65). The mean total WS score was 3.32 (SD 1.98) for the schizophrenic patients, significantly higher than that for the controls (2.19, SD 1.18). Minor physical anomalies were compared between two schizophrenic groups, divided on the basis of age at onset, early onset schizophrenia (EOS, onset under age 18 years) group and late onset schizophrenia (LOS, onset at or above age 20 years) group. The mean total WS score was 3.92 (SD 1.86) in the EOS group, significantly higher than the 2.59 (SD 1.79) in the LOS group. Minor physical anomalies are an indirect index for early prenatal central nervous system (CNS) maldevelopment; the present study indicated association between minor physical anomalies and EOS, thus a relationship between early prenatal CNS maldevelopment and EOS. These results support the hypothesis that EOS constitutes a subset of schizophrenia in which neurodevelopmental damage is largely involved.