This study investigates mortality of sharks in a commercial longline fishery in Australia. To examine the rate and biological, environmental and technological factors contributing to at-vessel mortality, four setlines with 120 gangions possessing 'hook timers' were deployed daily (for 7h and 14h) using conventional gears from two commercial fishing vessels during 2013. A total of 689 animals across 22 species and including 18 elasmobranchs were landed. For the five species (Carcharhinus spp.), and one genus (Sphyrna spp) where there were sufficient numbers for analysis, generalised linear mixed models showed that species and the elapsed time spent on the line after hooking were the strongest predictors of at-vessel mortality, with spinner (Carcharhinus brevipinna), blacktip (C. limbatus) and hammerhead (Sphyrna spp) sharks exhibiting the highest death rates. The variables which best explained mortality, included: (i) sex of the caught sharks, and the interaction between species with (ii) capture depth, and (iii) the elapsed time spent on the line after hooking. For the subset of dusky (C. obscurus) and sandbar (C. plumbeus) sharks examined for physiological status at the point of capture, very few of the 13 chosen blood analytes varied significantly. Given the observed high mortality rates and stress associated with the time spent on the line after capture, operational changes to reduce these adverse impacts should be considered. Even simple changes such as shorter soak times could considerably mitigate these impacts.