In the eutrophicated Baltic Sea, several naturally produced hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been found in marine biota. OH-PBDEs are toxic to adult and developing zebrafish and shown to be potent disruptors of oxidative phosphorylation (OXPHOS). Disturbed OXPHOS can result in altered energy metabolism and weight loss. In herring, the concentration of OH-PBDEs (i.e. 2'-OH-BDE68 and 6-OH-BDE47) has increased during the period 1980-2010 in the Baltic Proper. Over the same time period, the condition and fat content in Baltic herring have decreased. Given the toxicity and increasing trends of OH-PBDEs in Baltic herring it is important to further assess the exposure to OH-PBDEs in Baltic herring. In this study, the concentrations of OH-PBDEs and related brominated substances i.e. polybrominated phenols (PBPs), polybrominated anisoles (PBAs), methoxylated polybrominated diphenyl ethers (MeO-PBDEs) and polybrominated diphenyl ethers (PBDEs) were measured in herring sampled in the northern Baltic Proper (Askö, n = 12) and the southern Bothnian Sea (Ängskärsklubb, n = 12). The geometric mean (GM) concentrations (ng/g l.w.) at Askö and Ängskärsklubb were; Σ2PBPs: 4.3 and 9.6, Σ(2)PBAs: 34 and 20, Σ(6)OH-PBDEs: 9.4 and 10, Σ(7)MeO-PBDEs: 42 and 150, Σ(6)PBDEs: 54 and 27, respectively. 6-OH-BDE47 dominated the OH-PBDE profile and comprised 87% (Askö) and 91% (Ängskärsklubb) of the ΣOH-PBDEs. At Ängskärsklubb the mean concentration of ΣMeO-PBDEs (150 ng/g l.w.) was 15 times higher than ΣOH-PBDEs. As other fish species are known to metabolically transform MeO-PBDEs to OH-PBDEs, high levels of MeO-PBDEs can be of concern as a precursor for more toxic OH-PBDEs in herring and their roe.