OBJECTIVE Melanocytomas of the eye are typically benign tumors that may be associated with nevi and melanomas. In this study, we assessed the genetic data of melanocytomas and compared them with nevi and melanomas of both the eyes and the skin. DESIGN We microdissected 8 melanocytomas, 13 uveal melanomas, and 10 cutaneous melanomas and analyzed loss of heterozygosity markers on chromosome bands 1p36, 6q22-23.3, 9p21, and 10q23, which represent genetic loci associated with advanced dermal melanocytic lesions. RESULTS There was no loss of heterozygosity in any of the melanocytomas. However, many loss of heterozygosity events were found in uveal and cutaneous melanomas, most frequently involving chromosome 1 damage followed by chromosome 9 and 10 alterations. CONCLUSION Based on the absence of loss of heterozygosity in melanocytomas, specifically the locus that is lost most often in dysplastic nevi of the skin, we conclude that melanocytomas represent an entity that is different from melanomas or may be similar to that of dermal benign nevi. CLINICAL RELEVANCE Our results confirm that melanocytomas represent nonagressive lesions that do not demand radical surgery.