Infertile men are frequently affected by physical abnormalities that might be detected on routine general and genital examinations. These structural abnormalities might damage or block the testes, epididymis, seminal ducts or other reproductive structures and can ultimately decrease fertility. Physical deformities are variable in their pathological impact on male reproductive function; some render men totally sterile, such as bilateral absence of the vasa deferentia, while others cause only mild alterations in semen parameters. Concise and up-to-date information regarding the contemporary epidemiological characteristics, clinical features and pathophysiological impacts of these common abnormalities on male fertility is crucial for the practicing urologist to identify the best treatment option.