1. Paired trials were undertaken to compare toothfish catch rates and by-catch composition on Spanish system longlines with those on ‘trotlines’ fitted with cetacean exclusion devices (cachalotera nets). 2. CPUE (kg/1000 hooks and kg/set) was greater for trotlines than Spanish system lines when cetaceans were present. This difference increased with increasing abundance of cetaceans highlighting the potential of this gear to reduce cetacean depredation. 3. By-catch to catch ratio was greater by number for Spanish system lines when cetaceans were present during hauling. 4. A large percentage of skates caught on trotlines fitted with cachalotera nets were dead or suffered life-threatening injuries. Toothfish were also in much poorer condition to the extent that they were unsuitable for tagging and releasing. 5. Consequences of a move to trotlines would therefore lead to: i. Some positive benefits by reducing cetacean depredation. ii. Significant problems in understanding the meaning of CPUE for trotlines, and consequently in understanding CPUE trends unless there is an extended period of overlap between Spanish system, autoline and trotline use. iii. Potential increases in skate and toothfish injury, leading to problems with skate discard survivorship and achievement of tagging goals.