Protein digestibility is a key factor in the determination of protein quality using the chemical score. Since there are several methods available for determining protein digestibility the purpose of this study was to compare three methods in vitro (pH drop, pH stat and pepsin digestibility) and two methods in vivo (true and apparent digestibility in rats) in the determination of the protein digestibility of: casein, soy protein isolate, fish meal, black beans, corn meal and wheat flour. The results showed that in the case of highly digestible proteins all methods agreed very well. However, this agreement was much less apparent in the case of protein with digestibilities below 85%. As a result, the chemical score of these proteins varied substantially depending upon the method used to determine its digestibility. Thus, when the chemical score of the proteins analyzed was corrected by the true protein digestibility measured in rats, they ranked as: casein 83.56, soy 76.11, corn-beans mixtures (1:1) 58.14, fish meal 55.25, black beans 47.93, corn meal 46.06 and wheat flour 32.77. In contrast, when the chemical score of these proteins was corrected by the pepsin digestibility method, the lowest quality was assigned to fish meal. In summary, this results pointed out that for non conventional proteins of for known proteins which have been subjected to processing, protein digestibility should be measured in vivo.