Background: Although previous reports have described the association of autism, mental retardation, and schizophrenia with a missing Y chromosome, we are not aware of any case showing an association between this particular chromosomal abnormality and Asperger syndrome. Method: We report the case of a male patient with a combination of Asperger syndrome, obsessive-compulsive disorder and 45,X/46,XY mosaicism. During the follow-up, this individual has also developed a severe episode of major depression, which was successfully treated with electroconvulsive therapy. Results: To the best of our knowledge, this is the first case in which a 45,X/46,XY mosaicism was described in association with Asperger syndrome, either alone or associated with other psychiatric disorders. Diagnostic and therapeutic aspects of this unique case are presented and discussed. Conclusions: Our findings suggest that a missing Y chromosome may play an etiological role in some cases of Asperger syndrome.