Among the structural abnormalities affecting the human Y chromosome, dicentric chromosomes are the most common. A wide spectrum of phenotypes of patients with a dicentric Y chromosome exists, ranging from almost males through mixed gonadal dysgenesis to females with Turner syndrome. Here, we describe an infant with mixed gonadal dysgenesis and mosaic karyotype 45,X/46,X,idic(Y)(qter-->p11.32:p11.32-->qter)/47,X,+2idic(Y) (qter-->p11.32:p11.32-->qter)/47,XYY. This was demonstrated by fluorescence in situ hybridization (FISH) analysis with whole Y chromosome painting (WCP-Y) probe. Molecular studies were performed on genomic DNA extracted from peripheral blood lymphocytes. To examine the sex determined region (SRY), azoospermia factor (AZF) region and deletion in azoospermia gene (DAZ), polymerase chain reaction (PCR) analyses were done with sequence-tagged site (STS) primers of 20 loci along the Y chromosome (SRY, DYS271, DYS148, DYS273, KALY, DYS212, SMCY, DYS215, DYS218, DYS219, DYS221, DYS223, DYS224, DYF51S1, DYS236, DAZ, DYS240), and all tested loci were found positive. Because of the possibility of a mutation in the SRY gene, we analyzed the PCR fragment by DNA sequencing and did not observe any mutation or nucleotide alteration. We present detailed molecular-cytogenetic characterization of a patient with idic(Y)(p11.32), and results are discussed with the previously described patients. As far as we know, this is the fifth report of a 46,X, idic(Y)(p11.32) karyotype and the first presentation with mixed gonadal dysgenesis and isodicentric Y. Since the correlation between phenotype and karyotype is not yet well defined, the clinical reports will be helpful in defining the phenotypic range of this chromosomal abnormality.