1. The aim of this study was to evaluate the amount and quality of genomic DNA isolated from embryos and their chorioallantoic membranes (CAM) and to investigate the utility of different PCR methods for identifying the sex of Japanese quail embryos. 2. Fertilised eggs were incubated at 37°C for 120 h and DNA was isolated from samples of embryos and CAM. Target regions of the CHD-W gene or XhoI repeat sequence were amplified by PCR and examined on agarose gels or by using a capillary electrophoresis system. 3. DNA samples from embryos had significantly higher OD260 values than those from CAM, while OD260/280 values were not significantly different between embryos and CAM. 4. Gender identification was not possible by PCR amplification of the CHD gene region or XhoI repeat sequences examined on agarose gels, whereas males and females of Japanese quail were distinguishable when PCR products of the CHD gene were separated by capillary electrophoresis. 5. The results showed that high molecular weight DNA could be isolated from both embryo and CAM of Japanese quail. DNA isolated from CAM could be used for molecular genetic studies where embryos would be used for other purposes, such as in situ hybridisation. A capillary electrophoresis system could be used for identifying the gender of Japanese quail embryos.