BACKGROUND Schizophrenia being one of the most debilitating and chronic psychiatric illnesses still puzzles researchers due to its complex aetiology. Currently, neurodevelopmental hypothesis of schizophrenia is widely accepted explaining aetiology of schizophrenia. As per this hypothesis abnormal neurological development during gestation and childhood due to various factors make the individual susceptible for development of schizophrenia later in life. Presence of minor physical anomalies (MPA) points towards abnormal neurodevelopment during gestation which increases the risk of developing schizophrenia in later life. Purpose of our study was to evaluate the presence of minor physical anomalies in patients of schizophrenia and compare them with healthy controls. METHODS This was a cross-sectional comparative study. 50 schizophrenic patients were selected from OPD (outpatient department) and the presence of minor physical anomaly in those patients was compared with 50 normal healthy control subjects using Waldrop’s minor congenital anomaly scale. Schizophrenic groups were also categorised into the early-onset group and late-onset group and mean score of Waldrop’s minor physical anomalies in both the groups were compared. Patients with family history of schizophrenia were compared with those without any family history of schizophrenia. RESULTS Minor physical anomalies were significantly higher in the schizophrenic group (mean = 2.4) as compared to healthy controls (mean = 0.87). Incidence of minor physical anomalies in the early onset group (mean = 3.91) was higher than the late-onset group (mean = 1.53) but the difference was not statistically significant. CONCLUSIONS As the incidence of minor physical anomalies is more in schizophrenia, presence of MPAs in asymptomatic patients can predict the risk of developing schizophrenia in later life.