The objective of this study was to determine the effect of soybean meal (SB) or canola meal (CM) with or without inclusion of micro-encapsulated sodium butyrate (MSB) in calf starter mixtures on gastrointestinal tract (GIT) development. Twenty-eight Holstein-Friesian bull calves (8.7 ± 0.8 d of age, 43.0 ± 4.4 kg at the start of the study) were blocked by date of birth and initial BW and fed 1 of the 4 pelleted starters containing (1) SB; (2) SB+MSB; (3) CM and (4) CM+MSB. Crude protein (CP) content of the starters was (%DM): 1) 21.9; 2) 21.7; 3) 20.7 and 4) 20.3. The CM constituted 35.2%, SB 24.2% and MSB 0.3% of the respective starters DM. Calves were fed milk replacer (MR, 21.7% CP) at 0.85 kg/d for 35 d and then 0.43 kg/d for following 7 d. Calves were weaned at 51.7 ± 0.8 d of age and were killed at 72.1 ± 0.9 d of age. The GIT was dissected for morphometry measurements and tissue samples were used for histological assessment and brush border enzyme activity determination. Data were analyzed as a 2 × 2 factorial design. Pre-weaning starter DMI was greater for SB compared with CM (256 vs. 229 g/d; P = 0.01) and tended to be greater for MSB supplementation (232 vs. 253 g/d, P = 0.06), but MR intake was not affected. Mucosa surface area in the cranial ventral sac of the rumen was less for MSB (950 vs. 1197 mm²/cm², P = 0.02). Jejunum tissue mass was lower for SB than CM (2.13 vs. 2.43 kg, P = 0.05). For calves fed MSB, aminopeptidase A activity tended to be greater in the duodenum (1.68 vs. 2.82 U/mg protein × 10⁻³; P = 0.07) and was greater in ileum (8.89 vs. 13.30 U/mg protein × 10⁻³, P = 0.02), and aminopeptidase N activity tended to be greater in the ileum (31.50 vs. 38.46 U/mg protein × 10⁻³, P = 0.07). The use of CM in comparison with SB may reduce pre-weaning starter intake and average daily gain at weaning. MSB might benefit the calf pre-weaning by increasing starter intake and activity of aminopeptidases. However, MSB did not affect ADG or starter intake after weaning, and papillae surface area in the ventral sac of rumen was reduced.