The semi-enclosed and brackish Baltic Sea has become heavily polluted by nutrients, anthropogenic organic and inorganic chemicals via human activities. Persistent organic pollutants (POPs) have been thoroughly investigated due to their linkage to toxic effects observed in Baltic biota. There has been far less focus on semi-persistent pollutants e.g. naturally produced oraganohalogen compounds (NOCs) and their disturbances in the environment. This thesis is aimed on assessment of levels and trends of naturally produced brominated compounds in Baltic biota; more specifically on hydroxylated polybrominated diphenyl ethers (OH-PBDEs), methoxylated PBDEs (MeO-PBDEs) and polybrominated dibenzo-p-dioxins (PBDDs). These, NOCs, may originate from production in algae and cyanobacteria. OH-PBDEs and MeO-PBDEs may also be formed as metabolites of polybrominated diphenyl ethers (PBDEs), i.e. well-known commercial flame retardants. High levels of OH-PBDEs, MeO-PBDEs and PBDDs are shown within Baltic biota (cyanobacteria, algae, mussels, fish), often in much higher concentrations than PBDEs which are possible anthropogenic precursors of OH- and MeO-PBDEs. The levels of OH-PBDEs, MeO-PBDEs and PBDDs are higher in the Baltic Sea than on the west coast of Sweden. Temporal and seasonal variations show fluctuations in concentrations of OH-PBDEs, MeO-PBDEs and PBDDs, possibly related with macroalgal life-cycles. OH-PBDEs, MeO-PBDEs and PBDDs are present in several filamentous macroalgae species, but considering the levels quantified, the time of peak exposure and the species life-cycle the macroalgae, Pilayella, Ceramium and Cladophora are suggested as major natural producers of OH-PBDEs and PBDDs. The high levels of OH-PBDEs, MeO-PBDEs and PBDDs in the Baltic Sea may affect numerous organisms in the ecosystem. The toxic effects of OH-PBDEs and PBDDs are of particular concern. This thesis stress the importance of assessing and monitoring these substances, since the exposure to OH-PBDEs and PBDDs, during summer, may cause acute effects in Baltic fish and wildlife. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: In press. Paper 4: Manuscript.