Most important infectious diseases which pose a risk to human health and life are associated with parasites transmitted by a variety of arthropod vectors, or from animal to man. Some of these (malaria, toxoplasmosis, leishmaniosis, dirofilariosis, alveococcosis, cystic echinococcosis) still represent a serious public health problem in many regions in the world. This review describes the epidemiological and clinical aspects of important parasitoses and fungal infections from a medical point of view. It should be emphasized that the development of invasive disease depends on both host (susceptibility/resistance) and parasite factors (pathogenicity/virulence); an immunocompromised state can favour opportunistic parasitic infections: toxoplasmosis, cryptosporidiosis, giardiosis, cyclosporidiosis, blastocystosis and strongyloidosis. This article highlights the role of free-living amoebae in the pathogenesis and transmission of human diseases, the high pathogenicity of Echinococcus multilocularis, and the growing importance of ticks as a reservoir and vector for numerous dangerous pathogens (e.g., Borrelia burgdorferi, Anaplasma phagocytophilum, Babesia microti). It also discusses the diagnostic problems of toxoplasmosis including cross-reactions in serological tests and reviews the search for new drugs and vaccines against toxoplasmosis. Attention is increasingly paid to the role played by the human microbiome in maintaining homeostasis and in the development of fungal infections. This review also presents the most common human superficial fungal infections and the role of Candida albicans infection in the pathogenesis of irritable bowel syndrome.