The aim of this article is to give an overview of the molecular methods used for detecting helminth parasites in the environment, their advantages as well as their limitations with examples of successful applications of these methods in different helminth classes. Molecular techniques represent a wide range of sensitive diagnostic tools in parasitology. Environmental monitoring is an essential element of epidemiological studies. Many helminth parasites depend on the environment for the completion of their life cycle. The abundance of their transmissive stages determines infection risks. The application of highly specific and sensitive monitoring methods allows gathering more precise epidemiological data.