Is there a difference between an atypical nevus and melanoma in situ?

Yes. The difference is determined by the histopathology. Unfortunately, consensus regarding the histologic definition of atypical nevi is lacking. When an atypical nevus has atypical melanocytic nevus cells at the dermal–epidermal interface, some of these cells may exhibit cytologic atypia, but this is variable and not continuous throughout the lesion. There are also often architectural abnormalities noted between melanocytic nests. In contrast, melanoma in situ has atypical melanocytes, both singly and in small nests scattered through all levels of the epidermis (pagetoid pattern). Further, a typical melanoma is often more asymmetrical; melanocytes present as solitary units in the epidermis rather than in nests, and the melanocytes demonstrate a greater degree of cytologic atypia.