Using a multiplex nested polymerase chain reaction (PCR) method with single copy genes and a dinucleotide repeat locus for the mouse Y and X chromosomes respectively, it was possible to discriminate between single cells derived from male and female embryos. Using single cells, amplification of Sry and Zfy sequences was not evident in all cases. It could be calculated that, with the PCR method used, 0.04% [95% (confidence interval 0.00-2.03)] of the male embryos would erroneously be diagnosed as female if analysis is performed on two cells. The calculated chance for total amplification failure, if two cells are used for analysis, would be 1.4% [95% (confidence interval 0.04-8.04)]. The mouse embryo model proved to be a helpful tool to develop skills in the application of PCR for preimplantation genetic diagnosis at the single cell level.