Melanocytic nevi located on specific regions of the body can demonstrate unusual histopathological features such as asymmetry, irregular nesting patterns, pagetoid spread, cytologic atypia, and rarely, mitotic activity. However, despite these features that may raise concern for malignant melanoma, these lesions follow a benign clinical course and do not require intervention. Also known as nevi of special sites or nevi with site-related atypia, these melanocytic nevi were initially described on acral sites and genitalia. Now, additional anatomical sites with known site-related atypia include the ear, conjunctivae, scalp, breast, flexural skin, legs, and back and shoulder. This continuing medical education article presents a review of the histopathological characteristics of special site nevi based on anatomic location. It is imperative for dermatologists, pathologists, and dermatopathologists to distinguish benign melanocytic nevi with site-related atypia from malignant melanoma to avoid unnecessary surgical intervention or treatment.