Despite screening, effective anti-viral drugs and risk-balanced prophylaxis, cytomegalovirus (CMV) remains a major cause of morbidity in transplant patients. The objective of this study was to retrospectively analyze the risk factors associated with CMV viremia after kidney transplantation in a large European cohort with standardized valganciclovir prophylaxis in the present era. A special focus was placed on the comparison of living and postmortal donation. We conducted a longitudinal observational study involving 723 adult patients with a total of 3292 patient-years who were transplanted at our center between 2007 and 2015. Valganciclovir prophylaxis was administered over 100 days for CMV+ donors (D) or recipients (R), over 200 days for D+/R−, and none in D−/R−. A CMV+ donor, rejection episodes, and deceased donor transplantation were identified to be associated with increased incidences of CMV viremia. Although we did not find a reduced overall survival rate for patients with CMV viremia, it was associated with worse graft function. Since we observed a relevant number of CMV infections despite prescribing valganciclovir prophylaxis, a pre-emptive strategy in patients with (suspected) adherence restrictions could be favored. Our data can help transplant physicians educate their patients about their individual CMV risk and choose the most appropriate CMV treatment approach.