Infection and inflammation are relevant entities of male factor infertility. Bacterial infections are mostly the consequence of an ascending infection of the genito-urinary tract which can ultimately lead to epididymo-orchitis. Bacterial toxins and the innate immune responses directed against them may have a significant impact on male reproductive function. Toll-like receptors (TLRs) constitute the major family of pattern recognition receptors that play a pivotal role in innate immunity. In the testis, TLRs are not only found in immune cells such as macrophages and dendritic cells, but also in testicular somatic cells and to a lesser extent in germ cells. In this review we describe relevant bacterial pathogens found in testicular and male reproductive tract infection, new data on the localisation and potential functions of TLRs, recognition and response to bacteria with a special emphasis on uropathogenic Escherichia coli. Mechanisms by which uropathogenic E. coli subvert innate immune responses in the testis are discussed using information derived from animal model studies.