Background Isolation of adequate numbers of fetal cells circulating in the maternal circulation is the major hurdle in developing noninvasive prenatal diagnostic procedures. We used flow cytometry and a combination of different monoclonal antibodies to compare the yield and purity of the fetal nucleated red blood cells at different periods of gestation. Methods Using a Percoll discontinuous gradient, the fetal nucleated erythrocytes were enriched from 7 ml maternal blood. In 100 samples, the enriched cells were stained with CD45, anti‐fetal hemoglobin, and glycophorin A antibodies and in 30 samples they were stained with CD45, anti‐fetal hemoglobin, and CD71 and then sorted and used for fetal diagnosis of hemoglobinopathies. Results Using the first set of antibodies, although we were able to obtain a higher percentage of fetal nucleated red cells (0.07% ± 0.2%) as compared to the second set which yielded comparatively smaller numbers (0.025% ± 0.03%), there was some compromise in purity. Conclusion Using CD45, anti‐fetal hemoglobin and CD71 would be preferred as minimizing maternal contamination is more important than yield for prenatal diagnosis. © 2008 Clinical Cytometry Society