Today, weaner diets are optimised using digestibility coefficients obtained from grower-finisher pigs, which may overestimate the digestibility in weaners. The aim of this study was to evaluate the standardised ileal digestibility (SID) of CP and amino acids (AAs), and the intestinal morphology in pigs 0-4 weeks postweaning when fed different protein sources. The experiment included 128 pigs weaned at day 28 and the protein sources were wheat, soybean meal (SBM), enzyme-treated soybean meal (ESBM), hydrothermally treated rapeseed meal (HRSM) and casein. The experiment was conducted as a difference method study including wheat in all diets. Eight pigs were slaughtered on the day of weaning (day 0) and six pigs/treatment were slaughtered at days 7, 14, 21, and 28 postweaning. The SID of CP and AA, as average over the four weeks, was lowest for ESBM and highest for wheat and casein, with SBM and HRSM being intermediate. The SID of CP and AA increased (both linear and quadratic, P < 0.05) over time after weaning. The average SID of CP for all protein sources postweaning was 0.38, 0.59, 0.76, and 0.71 on days 7, 14, 21, and 28, respectively. These differences were significant (P < 0.05) between days 7 and 21, and between days 7 and 28 (P < 0.05), whereas there tended to be a difference between days 7 and 14 (P = 0.06). Protein source did not affect the small intestinal morphology response parameters, whereas time after weaning did. Villous height and villous height to crypt depth ratio differed (P < 0.05) between the days 0 and 7, with shorter villi and a higher ratio at day 7. Crypt depth was not altered between days 0 and 7, or between days 7 and 14. For villi density, crypt density and small intestinal length, a significant increase from days 7 to 14 was observed, but there was no further increase to or difference between days 21 and 28. In conclusion, the low SID of CP in casein on day 7 (0.50) illustrates the challenges related to protein digestion in weanling pigs. The SID of CP and AA is very low during the first two weeks postweaning and time after weaning is more important for protein digestibility, than the source of protein. Fewer mature epithelial cells and less absorptive area in the small intestine in the early postweaning period may partly explain the poor protein digestibility.