Fauna-free sheep, equipped with a rumen cannula and a duodenal re-entrant cannula, were fed a corn silage diet supplemented with casein (CA diet) or soybean meal (SBM diet). Eighteen days later the sheep were inoculated via the rumen cannula with a mixed population of ciliate protozoa. Rumen fluid and duodenal digesta were sampled for 4 d before the inoculation and for 13 d following the inoculation. A stable protozoal population was established within 8 d. Protozoa increased (P < 0.05) the digestion of organic matter in the stomach of sheep fed both the CA and the SBM diet, but the effects of supplemental protein and protein × protozoa interaction were not significant (P > 0.05). The stomach digestion of acid detergent fibre was not affected (P > 0.05) by protozoa or by the source of supplementary protein, but the protein × protozoa interaction was significant (P < 0.05). The disappearance of nitrogen from the stomach was lower (P < 0.01) for the SBM diet than for the CA diet and was increased (P < 0.05) for both diets in the presence of protozoa, but the effect of protein × protozoa interaction was not significant (P > 0.05). The ruminal presence of protozoa decreased the flow from the stomach of individual amino acids (from P < 0.05 to P < 0.001) and of nonammonia nitrogen (P < 0.05). However, the decreases were greater (from P < 0.05 to P < 0.001) for the CA diet than for the SBM diet, but the effects of protein × protozoa interaction were not significant (P > 0.05). The ruminal presence of protozoa increased (P < 0.05) the flow from the stomach of ammonia-N for SBM diet but not for CA diet. The effects of protein and of protein × protozoa interaction were not significant (P > 0.05). It was concluded that although ruminal protozoa do not metabolize casein, their effect of decreasing amino acid flow from the stomach can be greater for diets containing casein (soluble protein) as protein supplement than for those containing soybean meal (insoluble protein). Key words: Duodenal flow, nitrogen, protozoa, casein, soybean meal, sheep