The roles of inflammation and/or infection of the male accessory sex glands are very important for the potential effects that these conditions may have on male fertility. The clinical andrologist should be aware of the pathophysiological role of the main determinants of sperm damage when these conditions occur, in particular, seminal leukocytes, oxidative stress and cytokines. In addition, it is important to have a good knowledge of the methodologies to be used in clinical practice. This article summarizes the methods used to look for and to identify the micro-organisms responsible for male urogenital tract infections. These include sperm culture, urine culture, urethral swabbing, the Meares-Stamey test and balanopreputial swabbing. Finally, we discuss the role of human papilloma virus infection in male infertility.