Background Lymphocytic pleural effusions of unclear etiology are frequent after lung transplantation and are associated with adverse outcomes. Reactivation of human herpesviruses, in particular Epstein-Barr Virus (EBV), has been demonstrated to account for a share of unclear pleural effusions in immunocompetent and -compromised patients. Here, we assessed the detection of human herpesviruses in a large lung transplant pleural effusion cohort. Methods A prospectively sampled cohort of 99 pleural effusions of 67 lung transplant recipients was analyzed for HSV-1, HSV-2, EBV, CMV, HHV-6 and HHV-7 by qPCR. Clinical characteristics were compared between virus-positive versus negative pleural effusions. RESULTS EBV could be detected in 35 %, HHV-6 in 19 %, CMV in 4 % and HHV-7 in 1 % of assessed pleural effusion samples, whereas HSV-1 and HSV-2 could not be detected. Median viral load for EBV was 1500 copies/ml, for HHV-6 1300 copies/ml and for CMV 163 copies/ml. Overall, no relevant differences were found comparing the characteristics of EBV-, HHV6- and CMV-positive versus negative pleural effusions. Conclusions Herpesviruses can be detected in low copy numbers in a share of lung transplant pleural effusions. However, they do not seem to account for the high rate of unclear lymphocytic effusions after lung transplantation.