Through cytogenetic analysis, heteromorphisms were detected in chromosomes 1,9,16 and Y and defined as non-phenotypic variations. The polymorphism in the centromeric heterochromatin region of chromosome 6 is a rare variant, and only five cases have been documented in the literature. In our study, we used cytogenetic and molecular techniques to detect an increase in the centromeric heterochromatin region in the short arm of both copies of homologous chromosome 6 in a premature ovarian failure (POF) case. The report of this case is important for determining the relationship between fertility and the frequency of rare variants of the centromeric heterochromatin region of chromosome 6 in the general population.