OBJECTIVE To describe the molecular and cytogenetic characterization of a de novo unbalanced Y;autosome translocation in a 45,X mentally retarded male. METHODS Descriptive case study and literature review. METHODS Tertiary medical center. METHODS A 17-year-old 45,X mentally retarded male with no stigmata of Turner syndrome. METHODS Molecular and cytogenetic investigations, physical examination, and hormonal assays. METHODS Cytogenetic analysis, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (CGH), and polymorphic DNA marker analysis. RESULTS The FISH showed a Y/18p translocation. Array CGH revealed a loss of distal chromosome 18p material and a loss of part of Yq material corresponding to deletions of chromosomal segments of 18pter-->18p11.2 and Yq11.221-->Yqter. Polymorphic DNA markers analysis showed that the X chromosome was of maternal origin and the deletion of 18p was of paternal origin. CONCLUSIONS This study confirms the usefulness of array CGH in the detection of subtle chromosomal rearrangements resulting in an unbalanced Y;autosome translocation.