Minor physical anomalies (MPA) are subtle anatomical deviations in a person's appearance, which may suggest an altered embryogenesis. It has been observed that patients with early onset schizophrenia (EOS) have a higher number of MPA, which could serve as biomarkers to predict the onset or prognosis of this disease. Although these can be numerous, the most relevant include those located in the head and mouth. There is little information regarding the relationship between functional neuroimaging studies and MPA in patients with schizophrenia, and for this reason the following case of a 16-year-old male adolescent is presented. The Waldrop Scale for minor physical anomalies gave a score of 6. The single photon emission tomography (SPECT) scan showed hyper-perfusion in the following areas: frontal lobe, bilateral orbital-frontal cortex, and caudate nuclei.