The permeability characteristics of 33 amphoteric drugs (about 64% zwitterions at physiological pH) were studied using the parallel artificial membrane permeability assay (PAMPA) at pH 6.5. The PAMPA data were modified to include the paracellular permeability component found in cellular monolayers based on a newly generalized version of a popular model devised for Caco-2 cells. These "in combo" PAMPA data were used to predict the human absolute bioavailability of the ampholytes. The analysis produced a good fit, with only five outliers whose transport properties, could be rationalized by (a) nonpassive permeability processes, (b) metabolic instability, and (c) the possible sensitivity to microclimate pH effects in the case of acidic ampholytes. With the exception of two compounds, all of the ampholytes with bioavailability <50% were predominantly transported by the paracellular route, surprisingly with several of the compounds having molecular weights exceeding 350 Da. ©2009 American Chemical Society.