Adeno-associated viruses (AAVs) are microorganisms capable of replicating in host cells only in the presence of a helper virus. Despite their defective nature, they exhibit broad tropism for various organs and have a ubiquitous distribution. There are no definitive data on the effects of these viruses on the human body under conditions of natural infection. For a long time, AAVs were considered nonpathogenic, even in immunocompromised individuals, which led to their use as vectors in gene therapy. Currently, evidence exists for both neutral interactions between AAVs and the human host, as well as for pathogenic and protective roles of these viruses. A growing body of evidence describes the involvement of AAVs in the oncogenesis of hepatocellular carcinoma, the development of hepatitis, including cases associated with gene therapy, and an increased risk of male infertility, adverse pregnancy outcomes, and spontaneous abortions. At the same time, beneficial effects on human health have also been reported, including the prevention of cervical cancer through suppression of human papillomavirus replication. The aim of this review is to present data on the diverse effects of AAVs on human health, with a focus on the natural history of AAV infection.