The organic mercury content of five commercially valuable fish species (cod, flounder, turbot, perch and herring) was determined by use of an in vitro digestion model in order to assess health risk of fish caught within the Polish Exclusive Economic Zone of the Baltic Sea. Concentrations of total mercury and organic mercury were measured in the muscle tissue of fish and in the products of two-stage gastrointestinal digestion, using atomic absorption spectroscopy (AMA 254). The highest concentrations of organic mercury were found in the muscles of predatory fish that dwell in near-bottom waters. Based on a bioaccessibility estimate obtained from the in vitro digestion model, it was found that only 26–62% of organic mercury, depending on the species of fish, was released into the intestinal lumen during the digestion of muscle. Therefore, to postulate the potential toxicity of fish, based on the organic mercury content of the muscle tissue ingested by consumers, is unfounded. The risk assessment should be carried out on the basis of another parameter – the bioaccessibility of organic mercury.