Background: During pregnancy a small number of fetal RBCs (Red Blood Cells) enter maternal blood without risk, and incidence of significant fetomaternal hemorrhage (FMH) and isoimmunization depends on how much fetal blood enters maternal circulation; the use of flow cytometer (FCM) in FMH detection is considered the best laboratory technique. Aims: To evaluate role of FCM in FMH estimation to optimize delivery protocols and decrease isoimmunization. Subject and Method: 100 pregnant women at labor were included, equally classified into early cord clamping (ECC) and delayed cord clamping (DCC) groups, each including 25 women delivered vaginally and 25 with caesarian section; the control groups included 20 non-pregnant females, 20 at 3 rd trimester and 20 neonates. Fetal RBCs were done on Becton Dickinson (B.D) FCM, and the reagents used were 5-Glutaraldehyde 0.5% Sigma cat. G5882, flouroscine isothiocyanite (FITC) anti-hemoglobin F (Hb-F) cat. 555748, anti-carbonic anhydrase, Triton-X100 solution and Alsever's solution cat. HFH-11, 0.1% phosphate buffer saline/bovine serum albumin (PBS/BSA). Statistical Analysis: Mann Whitney's U-test, Chi-squared, Fischer's Exact tests, and SPSS for windows version 15.0. Results: There was a significant increase in the volume of the FMH in the ECC compared to DCC groups (p < 0.0001), also in the vaginal delivery comparing to caesarian section subgroups within the DCC group (p < 0.01), and in the ECC compared to DCC within caesarian section subgroup (p < 0.02). Conclusion: Fetal RBCs estimation by FCM is good; perinatal laboratory test should be done in routine investigations, as a guide for obstetric techniques that can alter FMH volume and decrease subsequent isoimmunization.