Semen analysis is the corner stone in the basic evaluation of the man in the subfertile couple. The recent WHO manual identifies and recommends robust, controllable methods. However, the distribution of results from recent fathers and men in the general population introduces significant problems. This review discusses the pitfalls with reference limits and the proper use of such limits for the interpretation of semen analysis results. It is critical to understand the statistical basis upon which the assumptions of reference ranges and cut-off limits are built and the importance of standardising methods and practical laboratory training. These are indispensable for qualitative laboratory work as well as for future prospective studies aimed at providing prognostic information for spontaneous pregnancies and successful Assisted Reproductive Techniques (ART) treatment. Proper understanding of biological and physiological variability is also essential for the correct interpretation of semen analysis results. Understanding all the factors influencing semen analyses is of great importance for the development of the entire field of reproductive medicine.