The aim of this study was to investigate the effect of ionization on drug transport across the intestinal epithelium in order to include this effect in structure-absorption relationships. The pH-dependent permeation of one rapidly (alfentanil) and one slowly (cimetidine) transported basic model drug across Caco-2 cell monolayers was investigated. Both drugs had pK(a)values in the physiological pH range. The permeability coefficients (P(c)) of the model drugs were obtained at varying apical buffer pHs, thus varying the degree of drug ionization (from 5 to 95%). The relationship between P(c) and the fraction of the drug in un-ionized form (f(u)) was analyzed to delineate the permeability coefficients of the un-ionized (P(c,u)) and ionized (P(c,i)) forms of the drugs. Theoretical estimates of the pK(a) values were also calculated from ionization energies for each model compound. For both drugs, a linear increase in P(c) was observed with increasing f(u). Transport of the un-ionized form was 150- and 30-fold more rapid than transport of the ionized form for alfentanil and cimetidine, respectively. However, when f(u) <0.1, the contribution of the ionized form was significant. Because f(u) is <0.1 over the entire physiological pH range for a large number of drugs, these results will have implications on predictions of in vivo intestinal drug absorption both from in vitro studies in cell cultures and from computed structural properties of drug molecules.