Fisheries by-catch is considered to be a major threat to loggerhead turtles in the Mediterranean Sea. Technical differences in both gear configurations (e.g. hook and bait type) and fisheries operations carried out by the Spanish Mediterranean surface longline fleet could have an effect on by-catch rates and size selectivity. The aim of the present study was to test the differences in by-catch per unit effort and body size of loggerhead sea turtles caught using different gear types in the Mediterranean surface longline fishery. Our results suggest that differences in the gear type used have an effect on catch rates and size selectivity. Thus, surface longliners targeting albacore (LLALB) using smaller hooks tend to capture smaller loggerheads but have the highest by-catch per unit of effort (BPUE), whereas other longlines, such as surface longliners targeting bluefin tuna (LLJAP) and traditional surface longliners targeting swordfish (LLHB), using larger hooks tend to select the larger animals; moreover, LLHB had the lowest BPUE. Disproportionate rates of fisheries-induced mortality on certain size/age-classes can differentially affect sea turtle populations, as each sea turtle age-class contributes differently to current and future reproduction. Thus, fisheries management should not only be focusing on preserving the large juvenile and mature turtles, but also on reducing the total by-catch. Thus, we recommend encouraging the use of LLHB versus other surface gears. We suggest that it is very important to take into account the gear type (and its particular catch rates) when making inferences about the impact of longline fisheries on sea turtle populations.