<b><i>Background: </i></b>Immunoprophylaxis with IgG anti-D is a standard prevention of hemolytic disease of the fetus and newborn. Fetal Rhesus D (RhD) blood group genotyping from maternal plasma of RhD-negative pregnant women allows targeted prophylaxis with IgG anti-D in RhD-positive pregnancies only. We set up a reliable protocol for prenatal <i>RHD</i> genotyping. <b><i>Methods: </i></b>153 pregnant Caucasian RhD-negative women were tested in the 27th week (range 7–38th week) of pregnancy. 18 of them were alloimmunized to the RhD antigen. The fetal <i>RHD</i> genotype was determined based on an automated DNA extraction and real-time polymerase chain reaction method. Intron 4 and exons 5, 7 and 10 of the <i>RHD</i> gene and the <i>SRY</i> gene were targeted. <b><i>Results: </i></b>The fetal RhD status and gender was 100% correctly predicted in all 153 pregnancies (55 RhD-positive males, 45 RhD-positive females; 23 RhD-negative males, 30 RhD-negative females). <b><i>Conclusion: </i></b>The accuracy and applicability of our protocol for non-invasive fetal RhD determination allows the correct management of RhD-incompatible pregnancies. Our protocol could prevent unnecessary immunoprophylaxis in 53 of 153 cases. We therefore recommend that non-invasive fetal <i>RHD</i> genotyping is introduced as an obligatory part of prenatal screening.