Heavy metal (HM) pollution has become one of the important threats to biological processes occurring in soil and to soil microbiota. This threat also extends to the active component of the soil microbial biota-fungi. In soils polluted with HMs, fungal communities undergo significant structural changes, leading, in particular, to an increase in the proportion and diversity of HM-resistant fungi, among which opportunistic human pathogens and facultative plant pathogens are found. The strains of fungi opportunistic for humans isolated from polluted soils have pathogenic properties to a greater extent than the strains isolated from clean soil. The implementation of pathogenic properties is determined by a number of molecular factors (virulence factors), among which are the activity of certain groups of enzymes, the action of antioxidant defense mechanisms and effector proteins, the synthesis of melanin and toxins, and modification of the lipid and carbohydrate composition of the cell. Heavy metals and soil pollution with them can influence the implementation of the pathogenic properties of fungi and fungus-like organisms that are toxic for humans, animals, and plants. This review provides data from the literature on molecular virulence factors and their modifications under the influence of HMs. Considering that at the moment there is no clear understanding of the direction of the action of HMs on the implementation of pathogenic properties by fungi, the literature data analyzed can still contribute to understanding the consequences of soil pollution with HMs for the development of opportunistic human pathogens and facultative phytopathogens.