Assessment of human ejaculate characteristics is a cornerstone in the evaluation of male fertility and in investigations of the function of the male reproductive organs. However, to evaluate the quality of results provided by a laboratory performing semen analysis, it is important for the clinician to have a thorough understanding of the physiological and biological basis for the formation and transport of spermatozoa and the process of ejaculation, as well as an understanding of basic aspects of laboratory science related to analysis of the human ejaculate. Consideration of causes for variability that is not based on pathology is thus also important for the clinician. This chapter does not aim to be a complete laboratory handbook but to give a guide for the clinician to understand strengths and weaknesses of semen analyses. With knowledge of the principles for modern laboratory medicine integrated into basic semen analysis, the clinician has a basis for evidence-based care for the patient whether investigated for infertility or for other diseases or disorders affecting the male reproductive organs.