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Two ultrafiltered soy flour protein fractions were evaluated; the first was obtained by hydrolysis (0.5–3 kDa, F0.5–3), and the second was an enzymatically methionine-enriched fraction (1–10 kDa, F1–10E). Amino acid profiles, protein quality, allergenicity (against soy-sensitive infant sera) and trypsin inhibitor activity were determined. Fraction F1–10E fulfilled amino acid requirements for infants, whereas the F0.5–3 fraction was methionine deficient. Both fractions were similar in net protein utilization, and F1–10E digestibility was comparable with casein and higher (P<0.05) than F0.5–3 or soy isolate. Allergenicity of SF was reduced to 21.5% with the hydrolysis in F1–10E and it was not detected in F0.5–3. Residual trypsin inhibitor activity with respect to soy flour was 8.1%, 3.3% and 1% for hydrolysate, F1–10E and F0.5–3, respectively. Both fractions presented high nutritive quality and reduced or null allergenicity. The trypsin inhibitor activity decreased along processing and could be a useful indicator for production of hypoallergenic proteins.