Male infertility affects 10% of couples of reproductive age worldwide, and is treatable in many cases. In addition to well-established etiologies, genetic causes of male infertility are now diagnosed more commonly, as our knowledge of genomic medicine advances. Using principles of evidence-based medicine, this review outlines diagnostic and treatment algorithms that guide clinical management. In order of importance, randomized controlled clinical trials, basic scientific studies, meta-analyses, case-controlled cohort studies, best-practice policy recommendations and reviews from peer-reviewed literature were incorporated into algorithms that provide organized and timely guidelines to the current management of male infertility. The strength of the evidence for treatment recommendations is also classified when appropriate.