Dioecious species that reproduce by internal fertilization typically carry an associated risk of exposure to sexually transmitted parasites and pathogens. When hosts intermingle for procreation, certain protist and helminth parasites, for example, transfer successfully between individuals and then navigate across various life history traits of their hosts, often probing dimensions in both sex and gender, respectively. In humans, there are many sexually transmitted infections as well as sexually transmitted diseases. A well-known sexually transmitted infection is the flagellated protist Trichomonas vaginalis that causes trichomoniasis, with over 150 million new cases reported annually. By contrast, the schistosome blood fluke Schistosoma haematobium, though not a sexually transmitted infection, causes significant damage to the male and female genital tracts. Such overt damage raises risks of spreading and acquiring Human Immunodeficiency Virus and Human Papilloma Virus. In Africa, over 50 million women continue to suffer from female genital schistosomiasis, alongside a poorly quantified global burden of travel-related infections. In conjunction with male genital schistosomiasis, urogenital schistosomiasis causes much suffering, within and between afflicted households, inclusive of stigmatization. Both trichomoniasis and schistosomiasis expose several public health needs currently addressed inadequately by routine sexual and reproductive health services. This preface to the Parasitology Special Issue entitled ‘Parasites of the genital tract: short- and long-term consequences’, introduces 19 papers that explore the short – and long-term impacts of parasitic infections within the genital tract. While current parasitological research is weighted towards human medicine, we encourage future studies that explore veterinary contexts and analogous parasitic diseases within wildlife.