Introduction: Determination of RhD variants in blood donors, pregnant women, and newborns is important for transfusion strategies, in order to prevent RhD alloimmunisation and hemolytic disease of fetuses and newborns. Implementation of molecular RHD typing in two transfusion institutes is presented in this article, from Banja Luka (Bosnia and Herzegovina) and Belgrade (Serbia). Study Design and Methods: Blood donors’ RhD was checked by direct agglutination assays (tube) and indirect antiglobulin test (gel). Molecular RHD typing was performed by PCR-SSP with fluorometric signal detection in both centres. Donors were selected by weak RhD serological reactivity (Banja Luka, 85 samples; Belgrade, 62 samples) or serologically RhD-negative C/E-positive results (Banja Luka, 92 samples; Belgrade, 61 samples). Results: Among serologically determined weak D donors from the institute from Banja Luka, weak D type 3 was the most frequent (58.8%), followed by type 1 (35.3%) and DNB (1.2%), whereas results obtained at the Belgrade institute were distributed between weak D type 1 (41.9%), type 3 (30.7%), type 14 (6.5%), type 15 (1.6%), and DNB with anti-D (1.6%). In 17.7% of serologically typed weak D samples from the Belgrade institute, the molecular typing result was standard D. Additionally, RHD presence was detected in 9.8% of serologically RhD-negative, C/E-positive samples from both institutes. Conclusion: Rh molecular testing was successfully implemented in both blood transfusion institutes in Banja Luka and Belgrade. This study proved the efficiency of serological algorithms for weak D, as well as the presence of the RHD gene among serologically tested RhD-negative, C/E-positive samples.