This paper describes a method for quantifying the functionality of the digestive system in fish larvae. The system described can provide data for the gut absorption, oxidation and retention (assimilation) of nutrients. A tube-feeding setup (originally described in Aquaculture 116 (1993) (341–352) using 14C-labelled dietary nutrients formed the basis of a new incubation system. This permitted unabsorbed nutrients evacuated from the gut to be distinguished from molecules originating from catabolism of the absorbed nutrient, both of which are present in the incubation water. The system is based on the release, transfer and entrapment of metabolically produced 14C–CO2 through manipulation of the water pH. The efficiency of the trap has been validated and tested, and provides 100.0±1.3% (S.D.) recovery. The usefulness of the method is demonstrated in a study in which Atlantic halibut post-larvae (46 days post first feeding) were fed a 14C-labelled protein diet. These data show that this protein has a digestibility of 42% for halibut post-larvae. If oxidation had not been measured through the use of the CO2 trap, digestibility would have been greatly underestimated (at about 25%).