Existing physiologically based toxicokinetic (PBTK) models for fish accurately predict the uptake and disposition of waterborne organic chemicals of low to intermediate hydrophobicity. These models have been used to evaluate factors that control chemical kinetics in fish and to extrapolate data among fish species. The utility of these models is limited, however, by a lack of understanding of the factors that control chemical uptake from dietary sources and an inability to measure, describe, and predict metabolic biotransformation. In this chapter, critical questions related to dietary uptake and metabolic biotransformation are identified and discussed. Research with fish that addresses some of these questions is presented. Guidance is also provided from modeling efforts with mammalian species. It is recommended that future research be directed towards developing a relatively simple gut sub-model description. In vitro methods for characterizing chemical biotransformation must be complemented by new techniques for measuring metabolism in the intact animal.