Purpose To evaluate hypotheses which explain phenotypic variability in sex determining region Y positive 46,XX males. We investigate two 46,XX males without gonadal ambiguities. Methods Cytogenetic and molecular analyses were used to identify the presence of Y chromosome material and to map the translocation breakpoint. Finally, the pattern of X chromosome inactivation was studied using the methylation assay at the androgen receptor locus.Results The presence of Y chromosome material, including the sex determining region Y gene, was demonstrated in both men. However, the amount of translocated Y chromosome material differed between the patients. Different X chromosome inactivation patterns were found in the patients; random in one patient and non-random in the other. ConclusionsWe found a lack of association between phenotype and X chromosome inactivation pattern. Our cytogenetic and molecular analyses show support for the position effect hypothesis explaining the phenotypic variability in XX males.