Testicular microlithiasis is an infrequent but well recognized condition, which is usually incidentally identified on testicular ultrasound scan. Interest in testicular microlithiasis has increased over the past few years, owing to an observed association with testicular germ cell tumor (TGCT) and intratubular germ cell neoplasia of unclassified type (ITGCNU). This association has added to evidence that testicular microlithiasis is a feature of the testicular dysgenesis syndrome (TDS), which is postulated to underpin disorders of male reproduction such as subfertility, testicular atrophy, cryptorchidism, TGCT and other abnormalities of sexual development. Although the genetic and environmental components of TDS remain unclear, studies of the molecular basis of TGCT support a genetic component for testicular microlithiasis and have identified multiple genes that are associated with TGCT. These advances in the biological understanding of testicular microlithiasis and TGCT have not, however, resolved key clinical dilemmas in the management of patients with these diseases. The role of testicular microlithiasis in the clinical consideration of testicular biopsy is discussed in the context of the apparently healthy individual, the individual with TGCT and the individual with TDS.