Complex small supernumerary marker chromosomes (sSMCs) consist of chromosomal material derived from two or more different chromosomal regions and constitute one of the smallest subsets of sSMC. Most of complex sSMCs are represented by a der(22)t(11;22) in Emanuel syndrome. As far as we know, only one recent report has described sSMCs involving simultaneously X and Y chromosomes in Turner Syndrome. We report two patients, a female and a male, both with a complex sSMC derived from X and Y chromosomes in mosaic with a 45,X cell line. In both patients, the marker chromosomes were early replicating and the XIST gene was absent. FISH and PCR confirmed the presence of Yp loci (TSPY, AMGY, SRY, DYZ3), and negative for DYZ1. The DAZ4 sequence was present only in patient 1. Our findings suggested that complex sSMC involving X and Y chromosome could be a kind of sSMC of the gonosomes.