Spitzoid melanocytic lesions encompass a spectrum from benign Spitz nevi to malignant spitzoid melanomas. Spitzoid melanocytic neoplasms have significant morphologic and molecular differences from conventional melanocytic lesions, and prediction of biologic behavior and metastatic risk may be difficult. Most challenging is the atypical Spitz tumor, a borderline spitzoid melanocytic lesion of uncertain malignant potential that has overlapping histologic features with conventional Spitz nevus and spitzoid melanoma. Atypical Spitz tumors involve the sentinel lymph nodes at a greater frequency than conventional melanoma and frequently harbor chromosomal copy number changes, yet most cases follow an indolent course. Herein we review the clinical, microscopic, and molecular features of atypical Spitz tumors, including recent molecular advances, including the potential prognostic significance of chromosomal abnormalities, such as homozygous CDKN2A loss.