The present study was undertaken to examine the relationship between chemical structure (steric and electrostatic fields) and affinity for the small intestinal oligopeptide carrier (PepT1) using comparative molecular field analysis (CoMFA), a three-dimensional approach towards building quantitative structure-activity relationships. Various biological activity parameters (Kt, Jmax, Pc) and molecular descriptors (CoMFA fields, isobutylalcohol/water distribution coefficients) were examined. The resulting field map provides information on the geometry of the binding site cavity and the relative weights of various properties in different site pockets for each of the substrates considered. The results indicate that carrier permeability (Pc), calculated as the ratio of the half-maximal concentration (Kt) and the maximal carrier flux (Jmax), is sensitive to composition, size and hydrophobicity of the ligands. The best model obtained showed a high correlation between the carrier permeability (Pc) and the steric (76.3% contribution) and electrostatic (23.7% contribution) molecular fields with a cross-validated r2 (q2) of 0.754. The model fitted the experimental data with a correlation coefficient of 0.993 and a standard error of 0.041, while the regression line between experimental and calculated Pc had a slope of 0.994 with an intercept of 0.009. These results lead to a better understanding of the molecular requirements for optimal drug-carrier interactions with the intestinal peptide transporter and offers a useful visual aid for designing new potentially interesting structures with affinity for the oligopeptide transporter PepT1.