Here we review the state-of-the-art of pathogens in select marine and terrestrial key species of the Baltic Sea, i.e.ringed seal (Pusa hispida), harbour seal (Phoca vitulina), grey seal (Halichoerus grypus), harbour porpoise(Phocoena phocoena), common eider (Somateria mollissima), pink-footed goose (Anser brachyrhynchus) and whitetailedeagle (Haliaeetus albicilla). This review is the first to merge and present available information and baselinedata for the FP7 BONUS BaltHealth project: Baltic Sea multilevel health impacts on key species of anthropogenichazardous substances. Understanding the spread, prevalence and effects of wildlife pathogens is important for theunderstanding of animal and ecosystem health, ecosystem function and services, as well as human exposure tozoonotic diseases. This review summarises the occurrence of parasites, viruses and bacteria over the past sixdecades, including severe outbreaks of Phocine Distemper Virus (PDV), the seroprevalence of Influenza A andthe recent increase in seal parasites. We show that Baltic high trophic key species are exposed to multiplebacterial, viral and parasitic diseases. Parasites, such as C. semerme and P. truncatum present in the colon andliver Baltic grey seals, respectively, and anisakid nematodes require particular monitoring due to their effects onanimal health. In addition, distribution of existing viral and bacterial pathogens, along with the emergence andspread of new pathogens, need to be monitored in order to assess the health status of key Baltic species. Relevantbacteria are Streptococcus spp., Brucella spp., Erysipelothrix rhusiopathiae, Mycoplasma spp. and Leptospira interrogans;relevant viruses are influenza virus, distemper virus, pox virus and herpes virus. This is of special importanceas some of the occurring pathogens are zoonotic and thus also pose a potential risk for human health.Marine mammal handlers, as well as civilians that by chance encounter marine mammals, need to be aware ofthis risk. It is therefore important to continue the monitoring of diseases affecting key Baltic species in order toassess their relationship to population dynamics and their potential threat to humans. These infectious agents arevaluable indicators of host ecology and can act as bioindicators of distribution, migration, diet and behaviour ofmarine mammals and birds, as well as of climate change and changes in food web dynamics. In addition, infectiousdiseases are linked to pollutant exposure, overexploitation, immune suppression and subsequent inflammatorydisease. Ultimately, these diseases affect the health of the entire ecosystem and, consequently,ecosystem function and services. As global warming is continuously increasing, the impact of global change oninfectious disease patterns is important to monitor in Baltic key species in the future.