There is a longstanding interest in describing the factors determining food chain length in ecological communities. Likewise, there has been considerable interest in explaining why food chain lengths differ in terrestrial and aquatic systems. The ‘energetic efficiency hypothesis' predicts endothermy and body size should be negatively correlated with food chain length. Using a large database of published food webs, we assessed the relationships between food chain length, endothermy, body size, and food-web structure. We utilized 77 published food webs spanning marine, freshwater, and terrestrial systems, ranging in species richness from 8–224 taxa. As expected, mean food chain lengths (MFCLs) in aquatic systems were significantly longer than those of terrestrial systems, even when comparing food webs of similar size and species richness. Endotherms were more numerous and occurred lower in terrestrial food chains compared to aquatic ones. Endotherms were also consumed by fewer predators and fed on more resources than ectotherms in terrestrial systems. This partially explains the decrease in trophic structuring and food chain paths in these systems (which was negatively correlated with MFCLs). The fraction of endotherms at the herbivore level was a strong predictor of MFCL in terrestrial systems, whereas the average difference in body mass between herbivores and their resources was the best predictor of MFCL in aquatic systems. This suggests that both body size and endothermy at the herbivore level play an important role in determining food chain lengths.