The mucus layer covering the surface of the gastrointestinal tract may act as a barrier to drug absorption. The aim of this investigation was to study the self-diffusion coefficients of model drugs with different physicochemical properties in gastrointestinal mucus. An in vitro method was used to determine the self-diffusion coefficients of radiolabeled model drugs in different diffusion media. Glucosamine, mannitol, glucuronic acid, glucose, metoprotol, antipyrine, propranolol, hydrocortisone, and testosterone, which display large differences in charge and octanol/water distribution ratios (K), were used as model drugs. The diffusion coefficients of model drugs were compared in phosphate buffer (PB), native pig intestinal mucus (PIM), and purified pig gastric much (PPGM). PIM was not purified and therefore contained all the original components of native mucus, whereas PPGM contained only high molecular weight mucin molecules. Charge had only minor effects on the diffusion coefficients of the model drugs. Lipophilicity, however, had a much larger effect, the largest decrease in diffusion coefficient, 58%, was observed for testosterone in PIM. A negative relationship between the diffusion coefficient and log K was observed in PIM, but no relationship was observed in PPGM and PB. In contrast, the diffusion coefficients for two larger molecules of comparable size, the lipophilic peptide cyclosporin and the hydrophilic peptide D-arginine vasopressin, were markedly reduced in PIM. In conclusion, the most important physicochemical characteristic influencing the diffusion coefficient of most drugs in gastrointestinal mucus appears to be lipophilicity, whereas molecular size appears to have more influence for larger peptide drugs.