The effect of pre-treatment was evaluated on the reduction in the content of dioxins (PCDD/F) and dioxin-like polychlorinated biphenyls (dl-PCBs) in the Atlantic salmon (Salmo salar) fillets and sea trout (Salmo trutta) caught in the Baltic Sea. The research studies included fish of different sizes. The levels of contaminants below the acceptable values as set out in the Commission Regulation (EU) No. 1259/2011 were found in the pre-treated products produced from salmon fillets of up to 7900 g in weight and up to 86 cm in length, and from the sea trout, their weight up to 4500 g and length up to 74 cm. In the case of the trimmed fillets (which contained the ventral part), the content of dioxins and dl-PCBs therein did not exceed the acceptable levels in the Baltic salmon of up to 2579 g in weight and up to 65 cm in length nor in the sea trout of up to 3376 g in weight and up to 65 cm in length. It was concluded that the pre-treatment process involving trimming and removal of the ventral part of fillet (about 25 % of weight) caused the content of contaminants in the final product to decrease. The study results indicate that the monitoring of contaminants in fish with the focus on consumer safety should involve samples of fish directly available to consumers in chain stores. In the case the sample is a whole fish, the procedure of preparing a sample for laboratory tests has a major impact on the final result of assay.