Studies have shown that minor physical anomalies (MPAs) may be associated with schizophrenia. However, it remains unclear whether any items of MPAs are more associated with schizophrenia than the others. We aimed to examine which specific MPAs are more associated with schizophrenia than others. A total of 154 patients with schizophrenia and 152 healthy controls were assessed using candidate MPAs items along with items from the Waldrop scale. Significant differences were found between the patients and controls in inner canthal distance, epicanthus, adherent ear lobe, cuspidal ear and length difference from section index to ring finger (2D:4D length difference) as well as gap between the first and the second toes. These six items were selected by the logistic regression model, which correctly classified 89.0% of patients with schizophrenia (sensitivity) and 96.7% of healthy controls (specificity). The overall classification success rate was 92.8%. MPAs are associated with neurodevelopment, especially 2D:4D associated with cerebral lateralisation. Hence, our present findings support that it is necessary to evaluate MPAs beyond the Waldrop scale, as some item, such as 2D:4D length difference may reflect the more detailed aberrant neurodevelopment of schizophrenia.