Several studies have identified bacteria and viruses in human prostatic tissues. The tumor microenvironment of prostate carcinoma is a complex community of genetically transformed cancer cells, non-neoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbes is the least well known. A variety of detection techniques have been used, such as PCR-based approaches, fluorescence in situ hybridization, immunological detection assays, and (bacterial) cultivation. Detection rates vary between these methods and each method has specific advantages and limitations. However, confounded by the high risk of contamination during or after the biopsy, it is challenging to make solid conclusions about the presence of certain microorganisms and its possible role in disease formation or progression. This doubt increases with the sensitive detection methods such as next generation sequencing technologies if there are no proper controls. Resident microbial communities often differ between healthy and diseased states, but whether these differences are of primary etiological importance or secondary to the altered inflammatory environment remains largely unknown.