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To specifically study the functional ontogeny of the digestive tract, larvae of Japanese flounder at various developmental stages were injected with liquid solutions using tube feeding in vivo. The survival in the stages tested was on average 93%. The injected solutions were almost completely transferred from the presumptive stomach, or stomach to the midgut within 10 min of injection. The passage to the hindgut in some cases started 10 min after injection and over 90% of the solution had passed from the midgut to the hindgut after 1 h. In most cases the hindgut seemed to be completely empty after 3 h. Two different mixtures of pH indicators with sensitivities in the alkaline (7.5 to 9) and acid (4 to 6) ranges respectively were used for assessment of pH in the various gut segments. The pH of the stomach remained alkaline during the larval period, but had fallen close to 4 during late metamorphosis, an indication of active HCl secretion and progressive stomach differentiation. In mid and late metamorphosing fish a rapid colour change in the pH indicator was observed once it had passed the pyloric sphincter. This demonstrates that there was also active secretion of alkaline fluid, most likely HCO3−, from the pancreas into the pylorus lumen. A single injection of liquid solution of 14C-FAA showed that assimilation of FAA was high in all stages tested (79.5 ± 7.1%; SD; n=91). The presently reported data for Japanese flounder support earlier studies that FAA are absorbed with a high efficiency in the early stages of marine fish.