The diagnosis and treatment of diseases caused by the exposure of human epigenome to environmental pollutants are hampered by epigenomic plasticity, instability and nonlinear cumulative effects of existing transcriptional regulatory pathways. DNA methylation, histone acetylation and histone methylation are the best studied epigenetic modifications. There are simple methods for assessing genome-wide DNA methylation; however, it is essential to study the epigenetic landscape in detail in order to uncover the mechanisms underlying pollutant-associated effects on the organism. This prompts researchers to employ whole-genome sequencing and analyze vast arrays of sequencing data that can be compiled into extensive databases of human and animal epigenomes. Drugs developed to counter epigenetic disorders neutralize their symptoms and either affect epigenetic modifications across the entire genome or regulate the activity of enzymes that play a critical role in such disorders. Promise is held by targeted genome editing methods supported by modern technologies that are undergoing preclinical trials. This review discusses the potential of modern science in the diagnosis and treatment of diseases caused by environmental pollutants.