The mosaic pattern of phylloid hypomelanosis is mostly associated with chromosome 13 abnormalities. Recently, 1 case of hypermelanosis in a phylloid pattern has been described. We describe a 29-year-old Japanese male with mental retardation, phylloid hypermelanosis and histopathologically and ultrastructurally peculiar melanocytic nevi, which were associated with 3 aberrant chromosome 13 cell lines. The karyotyping of 30 peripheral blood lymphocytes showed 46,XY,r(13)(p11.2q34) in 21 cells, 45,XY,-13 in 7 cells and 46,XY,dic r(13)(p11.2q34) in 2 cells. Immunohistochemical staining with HMB45 showed a positive reaction to basal keratinocytes in phylloid hypermelanosis. HMB45 staining reacted to the nevus cells and keratinocytes in the melanocytic nevi. Electron microscopy of a specimen excised from a melanocytic nevus showed an unusual finding of aggregated and disfigured melanosomes in the keratinocytes. This case suggests that chromosome 13 abnormalities may be related to the development of phylloid hypermelanosis and the bizarre melanosomes in the keratinocytes of melanocytic nevi.