We hypothesized that interleukin-6 (IL-6) in plasma and bronchoalveolar lavage (BAL) might serve as additional diagnostic parameter in lung transplant patients with human cytomegalovirus (HCMV) infection. Therefore, we compared IL-6 levels in HCMV-positive vs. HCMV-negative patients. IL-6 was measured by ELISA in plasma and BAL in 111 patients. Furthermore, we investigated the influence of IL-10 on IL-6 production in HCMV-positive patients. For HCMV-DNA detection in plasma and BAL a quantitative polymerase chain reaction (PCR) assay was used. IL-6 levels were significantly higher in the HCMV-positive group (n = 39; BAL p = 0.045; plasma p = 0.017) in comparison to the HCMV-negative group (n = 72). IL-10 did not correlate with IL-6 concentration (p = 0.146). Donor (D) or recipient (R) HCMV-constellation did not influence IL-6 concentration. IL-6 levels were not influenced by elevated levels of HCMV copies. Our data suggest that IL-6 does not serve as a good diagnostic parameter for existence of HCMV infection in lung transplant patients. Because of the wide range of the IL-6 levels in both groups, we were not able to find a breakpoint differentiating between infected and not-infected patients. Another important finding was that IL-6 production is not dependent of the HCMV status of D/R.