This study aimed to determine if cerebellar ataxia, hypogonadism and chorioretinopathy (AHCR) is associated with mutations in mitochondrial DNA or in genes responsible for spinocerebellar ataxias (SCA1, SCA2, SCA3 and Friedreich's ataxia). Two brothers with cerebellar ataxia, hypogonadism and chorioretinopathy and their unaffected parents underwent molecular analysis for duplications and deletions in mitochondrial DNA (mtDNA), point mutations in the ATP ase 6 gene, and expansions of CAG repeats (at 6p22-p23, 12q24.1, 14q32.1) and of GAA repeats (at gene X25 on chromosome 9q13). The research was negative for all mutations. Our findings confirm that AHCR is a distinct disease within the inherited cerebellar ataxias.