Pericentric inversion of Y chromosome has an estimated frequency of the one per thousand. This inversion is always inherited but also is possible a de novo presentation. Sometimes this inverted chromosome is associated with the Down, Klinefelter and other chromosomal syndromes. For the carriers of pericentric inversion the risk of the mental retardation or multiple abortion is not apparently increase and there is not relation with abnormal phenotypic features. The pericentric inversion of Y chromosome is only a rare chromosomal heteromorphism. Chromosome analysis of the father is advisable to determine whether or not the inversion is familial in order to be able to provide genetic counselling. Cytogenetic analysis from amniotic fluid cells and parents’ peripheral blood lymphocyte cultures were prepared by routine methods. Fluorescence in situ hybridization (FISH) was performed on cultured amniotic fluid cells to confirm the presence of Y-bearing cells. We performed molecular genetic analysis for Y chromosomal loci (SRY, ZFY, SY84, SY86, SY127, SY134, SY254, SY255). In cytogenetic analysis, the karyotype of male fetus, other brother’s and his father’s were exhibited as 46,X, +mar (Y), inv (Y) (p11.2;q11.23)?. His mother’s was 46, XX. In these cases, it was concluded that there was no clinical significance because the same abnormality was found in other members of the family. All of them have normavl phenotypic features. This finding suggests that the pericentric inversion of the Y chromosome affects neither the phenotype nor reproductive performance. ©2008, Firat University, Medical Faculty.