Background: Cytomegalovirus (CMV) remains leading to high morbidity and mortality in allogeneic stem cell transplant (Allo-SCT). High immunosuppression increases the risk of reactivation and allows repeated reactivation episodes. However, immunosuppression varies in accordance to donor types. In this study, we compared CMV reactivation in different Allo-SCT: Related (RD), unrelated (URD), and haploidentical (Haplo) donor SCT and analyzed the dynamic of repeated CMV episodes. Methods: Prospective cohorts of Allo SCT (from 2013 to 2019). Patients were screened by CMV quantitative PCR (Taqman Sistem – artus CMV Qiagen) in plasma. The screening started on the first week after SCT, repeated once a week until D+100, and after D+100 if immunosuppression was maintained. Repeated episode was defined if at least two negative CMV CRP results were obtained after the first episode. The following variables were analyzed: time after SCT to reactivation, initial viral load, highest viral load within the event, duration of viremia, and response to treatment. Results: There were 123 Allo-SCT performed. Median age was 47 years (ranging 1 to 70), and acute leukemia represented 63%. RD, URD, and Haplo were 72 (58%), 30 (24%), and 21 (17%), respectively. The median duration of follow-up was 251 days. CMV reactivation was documented in 84 (68%), with a median number of 2 (1 – 9) episodes per patient. RD, URD, and Haplo had similar frequencies of reactivation (64%, 70%, and 81%; p = 0.33). URD-SCT had earlier reactivation than others (median D+6, versus D+37 and D+ 21 in RD and Haplo, p < 0.001). A total of 192 CMV reactivation episodes were analyzed: 100 in RD, 55 in URD, and 37 in Haplo. Haplo-SCT reached the highest viral loads (median of 1070 copies/mL vs., 373 and 163 copies/mL in RD and URD-SCT; p = 0.036). First CMV reactivation episode reached higher viral load (median 1897 vs. 143 copies/mL; p < 0.001) and longer viremia (median 28 vs. 14 day; < 0.001), compared with repeated ones. Conclusions: Reactivation of CMV occurred with different dynamics by SCT donor type and in the first or repeated episode. Treatment and preventive strategies should be adapted, considering these different scenarios.