Ecological risk assessment is a useful methodology for assisting the management of fisheries from an ecosystem perspective. Atlantic tuna fisheries, managed by the International Commission for the Conservation of Atlantic Tunas (ICCAT), are economically important and interact with several bycatch species. In spite of these interactions, no comprehensive ecological risk assessment has been conducted for bycatch species caught in ICCAT fisheries. In this paper, we followed a two stage approach with the objective of assessing the relative risk of species being negatively impacted by Atlantic tuna fisheries. An analysis of the ICCAT bycatch species list (which includes all species reported to have interacted with different tuna fishing gears operating in the Atlantic) revealed that most of these species are caught in longline fisheries, followed by gillnets and purse seines. According to the IUCN red list, 7 species of the ICCAT bycatch list (3 coastal sharks, 3 sea turtles and one seabird) are categorized as critically endangered. In our study, and based on their life history characteristics, marine mammals and coastal sharks caught in ICCAT fisheries showed the highest intrinsic vulnerability values. A productivity susceptibility analysis for the European Union (EU) tropical tuna purse seine fleet and the United States (US) pelagic longline fleet revealed two groups with high relative risk scores. The first one included pelagic and coastal sharks, characterized by relatively low productivities, and the second one included teleosts, characterized by higher productivities but high susceptibility to purse seine and longline gears. Some alternative approaches to conduct productivity susceptibility analyses in the context of ecological risk assessments are discussed.