Several methods have been evaluated to partition feed crude protein (CP) into rumen-degradable protein (RDP) and rumen-undegradable protein (RUP) and to estimate the intestinal digestibility of RUP. These methods include in vivo, in situ, and a variety of in vitro methods. In situ-derived protein fractions were adopted for use to estimate RDP, RUP, and RUP digestibility in the most recent Dairy National Research Council model. In vitro, chemically determined protein fractions are used in the Cornell Net Carbohydrate and Protein System (CNCPS) that was subsequently adopted for use in level 2 of the Beef National Research Council model and in the Cornell-Penn-Miner (CPM) model (version 1). A comparison of the two methods for predicting RDP/RUP and RUP digestibility indicated remarkable similarity. Using data from 78 studies that reported measured flows of nonammonia nonmicrobial N (NANMN) to the small intestine of growing cattle and dairy cows fed 278 different diets, it was observed that the mean bias of prediction for NANMN was +1. g/d for NRC and -24. g/d for CNCPS. Whereas some disparity exists in predicted estimates of RUP for a few feeds, in most cases values are similar. To determine the impact of input uncertainty in the in situ protein system of NRC and the chemical partitioning method of the CNCPS on predicted metabolizable protein (MP) allowable milk and model-predicted RDP, a sensitivity analysis of the two models was conducted. For NRC, the highest variance in MP allowable milk was caused by variance in digestion rates of the B protein fraction, followed by the variance in the proportional sizes of the three CP fractions (i.e., A, B, and C), feed composition (e.g., CP), and RUP digestibility. For CNCPS, the highest variance in MP allowable milk was caused by the variance in feed composition, followed by the variance in the chemical components of feeds that affects the size of the five CP fractions in CNCPS (i.e., CP, soluble CP, neutral detergent insoluble CP [NDICP], acid detergent insoluble CP [ADICP], and nonprotein nitrogen [NPN]), RUP digestibility, and the digestion rates of the CP fractions. This analysis indicates that both models are sensitive to their respective inputs and that the size of the protein pools and the digestion rates of the potentially degradable protein fractions are strongly correlated to feed composition. Whenever possible, actual vs. model-default values for feed composition and pool sizes should be used.