Definition of chronic male genital tract inflammation and its impact on male infertility is still a matter of debate. In particular, DNA integrity has been reported to be disturbed in subfertile men. Thus, the aim of this study was to investigate an association of DNA integrity to altered standard semen parameters as well as inflammatory parameters such as peroxidase-positive cells, macrophages and seminal interleukin-6 concentration. Macrophages were detected by CD18/HLA-Dr staining, and DNA integrity was analysed by acridine orange staining using flow cytometry. Interleukin-6 was detected by ELISA. Normal DNA integrity showed a significant correlation to sperm number and progressive motility. Moreover, a significant inverse correlation of DNA integrity to Interleukin-6 and macrophages could be demonstrated. Further on, seminal interleukin-6 also significantly correlated to macrophages. No association has been observed between the number of peroxidase-positive cells and normal DNA integrity. As disturbed DNA integrity has been reported to negatively influence spermatozoon-egg interaction and even fertilisation rates following ICSI, and as early miscarriages have been associated with sperm DNA damage, it should be screened very carefully for male genital tract inflammations in couples undergoing infertility treatment. Measuring Interleukin-6 seems superior to assessment of the number of leucocytes alone and additional assessment of DNA integrity into the diagnostic work-up should be considered.