Evaluation of free plasma DNA has been suggested as one of the option to detect organ rejection in transplanted patients. However, the presence of chimeric cells in organs could make this approach complicated. To study the presence of Y-chromosome chimeric cells, we examined biopsy samples of 40 thoracic aortas of female donors and recipients. Using nested polymerase chain reaction, the presence of Y-chromosome-specific DNA sequences was detected in 19 (47.5%) analyzed tissue samples. Thus, free DNA originating from more than two genomes could be present in plasma in such a high proportion of cases. This phenomenon makes the use of plasma free DNA for the detection of organ rejection difficult and impractical.