Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder characterized by oculocutaneous albinism, a bleeding disorder, and ceroid lipofuscinosis in the lungs and gut. HPS is genetically heterogeneous and the most common variant, HPS type 1, is caused by mutations in HPS1 gene. The protein encoded by HPS1 is considered to facilitate the trafficking of melanocyte-specific gene products into the premelanosome. We report the ultrastructural findings in a melanocytic nevus seen in a 17-y-old Japanese female patient with HPS1 who is a compound heterozygote of HPS1 mutations, including a novel mutation. Electron microscopy of a pinkish papule corresponding to the melanocytic nevus revealed markedly aberrant, immature melanosomes, large membranous structures, and giant melanosomes in the vicinity of trans-Golgi network, the characteristic abnormalities because of protein trafficking defects in HPS1. These ultrastructural features were far more clearly demonstrated in the nevus cells than in the epidermal melanocytes. Thus, ultrastructural analysis of nevus cells may be an additional diagnostic tool for HPS1 and could give us important clues to further understanding of the pathomechanisms of HPS.