The authors presented the results of DNA polymorphism investigation of blood, buccal swabs and hair follicles originating from patients after allogeneic hematopoietic stem cell transplantation. The real-time and multiplex assays based on polymerase chain reaction within the range of autosomal as well as Y-chromosomal markers were applied to assess the possible dangers arising from investigation of these materials in forensic genetics. The results revealed that not only post-transplant blood and buccal swab, but also recipient hair, up to now regarded as devoid of any donor's cells, do not constitute entirely safe material for forensic purposes. Their analysis can lead to the false identification of gender or male haplotype. The investigation of sex-determining region Y and Y-chromosome short tandem repeats performed in female recipients with male donors resulted in the designation of donor's DNA in hair cells as well as in blood and buccal swabs. Therefore, biological stains gathered from crime scenes should not be analysed exclusively based on the investigation of male-specific markers.