The rearrangement of chromosome 6, particularly the deletion of 6q, has been observed in human malignant melanoma with or without brain metastases. The isochromosome 6p has also been described. In this study, we report the cytogenetic analysis of a primary malignant melanoma of the central nervous system. Its dominating karyotype was 47,XX,+i(6)(p10). Fluorescence in situ hybridization (FISH), using a 6p chromosome arm probe, confirmed the structure of the isochromosome. To our knowledge, this is the first report of this type of chromosomal aberration in an uncommon neoplasm of leptomeningeal melanocytic origin.