Epstein-Barr virus (EBV) is a lymphotropic herpesvirus causing clinically self-limiting but lifelong persisting infections. Although several severe diseases (e.g., Hodgkin's disease) are associated with EBV, its role in lower respiratory tract infections is still elusive. The prevalence of EBV, herpes simplex virus (HSV) and cytomegalovirus (CMV) in bronchoalveolar fluid (BAL) samples was evaluated in a retrospective study. BAL samples from 135 patients in the intensive or coronary care unit (ICU/ICC) at University Hospital Frankfurt/Main (Germany) were investigated using an in-house real-time PCR to detect EBV-, HSV- and CMV-specific DNA. Overall, herpesvirus DNA was detected in n = 82/135 BAL samples (60.7 %). Besides mono-infections with either EBV or HSV, concomitant infection with EBV and HSV DNA was most frequent, whereby the relative HSV viral load was typically higher. Patients with HSV-positive BAL required mechanical ventilation on average 5 days longer than patients with HSV-negative BAL (p = 0.006). Additionally, the proinflammatory cytokine IL-6 was significantly elevated in sera of patients positive for EBV in comparison with patients with EBV-negative BAL (p = 0.01). This study demonstrates a high prevalence of herpesviruses in BAL samples of ICU/ICC patients. The detection of one or more herpesvirus in BAL is strongly associated with the duration of ventilation and patient's age. The association between IL-6 levels and EBV detection should be evaluated in further studies.