Evidence is steadily accumulating to support a neurodevelopmental basis for pedophilia. This includes increased incidence of non-right-handedness, which is a result primarily of prenatal neural development and solidified very early in life. Minor physical anomalies (MPAs; superficial deviations from typical morphological development, such as un-detached earlobes) also develop only prenatally, suggesting them as another potential marker of atypical physiological development during the prenatal period among pedophiles. This study administered the Waldrop Physical Anomaly Scale to assess the prevalence of MPAs in a clinical sample of men referred for assessment following a sexual assault, or another illegal or clinically significant sexual behavior. Significant associations emerged between MPA indices and indicators of pedophilia, including penile responses to depictions of children, number of child victims, and possession of child pornography. Moreover, greater sexual attraction to children was associated with an elevated craniofacial-to-peripheral anomalies ratio. The overall sample demonstrated a greater number of MPAs relative to prior samples of individuals with schizophrenia as well as to healthy controls.