The effects of supplementing cereal-based diets with 0, 40, or 80 g of pectin (P) or 270 g of rye (R) per kg on ileal digestibility of protein and amino acids (AA), and digesta viscosity in pigs of 20 kg body weight (BW), and on growth performance, nitrogen balance, small intestinal morphology, and threonine metabolism parameters in pigs of 15 kg BW were assessed. Digesta viscosity was increased more by 80 g than by 40 g P or by R. Ileal digestibility of AA and nitrogen retention were negatively affected by P, whereas growth performance was decreased by R. The effect of the supplements on intestinal morphology was variable, except for the increase in myenteron thickness by P and crypt depth by R. The number of goblet cells containing acidic mucins was decreased by 40 g P in crypts in the mid-jejunum and by 40 g P and R in villi in the ileum. Fasting and postprandial plasma levels of free threonine and of threonine dehydrogenase activity in the liver and pancreas were not affected. In conclusion, feeding P or R negatively affects ileal AA digestibility and provokes irregular changes of small intestinal morphology. These effects cannot be attributed to the increase of digesta viscosity as the main factor.