The International Council for the Exploration of the Sea (ICES) listed the cod Gadus morhua as one of the target species for environmental biomonitoring in the Baltic, but only limited data on morphological biomarkers in this fish have been published so far. This pilot study examined cod tissues for the presence of selected biomarkers that have been studied in other target fish species for this region: flounder Platichthys flesus, herring Clupea harengus, and eelpout Zoarces viviparus. Twenty cod were collected in May 2012 off the Polish coast near Ustka. The biomarkers studied included condition factor, macroscopic lesions, morphometry of hepatic and splenic melanomacrophages, ovarian follicular atresia, and histopathology of spleen, liver, and gonads. All fish appeared in good body condition and had no macroscopic lesions except for one with multifocal dermal ulcers. Microscopic lesions were present in all fish, and included biliary myxozoanosis, ovarian microsporidiosis, larval nematodes compatible with Anisakidae, one case of intravascular trematodiasis, necrocentric granulomas, mild inflammatory and toxicopathic hepatocellular lesions, and marked accumulations of splenic melanomacrophages. This pilot study expands the types of microscopic lesions that have been documented as part of biomonitoring efforts in Baltic cod.