Concentrations of polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB) in Baltic Sea fish like herring (Clupea harengus membras), sprat (Sprattus sprattus balticus), perch (Perca fluviatilis), pikeperch (Sander lucioperca) and flounder (Platichthys flesus trachurus) collected from four areas of the Estonian coastal waters are reported. All samples are studied for their relationship between the length (cm) and wet weight (g); length (cm) and age (years); lipid content and dry matter. The level of PCDD/F and PCB concentrations in younger 1-5 years old Baltic herring and sprat collected in 2002-2005 from the eastern and central parts of the Gulf of Finland, Gulf of Riga and Open Baltic Sea (Central Baltic) is related to the fish age and compared with those found in the 1990s. In addition, PCDD/F and PCB concentrations of different age groups herring, sprat, perch, pikeperch and flounder collected in 2003-2004 from the Lake Peipsi, Gulf of Finland, Gulf of Riga and Open Baltic Sea are related also to their age. Consequently, it was manifested that in older Baltic fish the concentrations of PCDD/F and PCB were higher than in the younger age groups. By the help of principle component analysis (PCA) the effect of gender on the concentrations of PCDD/F for the juvenile Baltic herring and sprat collected in 2004-2005 is investigated for the first time. It was summarized that the biological factor age plays a large role for the contamination of the fish with important toxic organohalogenated compounds such as PCDD/F.