An experiment (complete randomised design) was conducted to investigate the effects of supplementing different molecular weights (MW) of chitooligosaccharide (COS) on intestinal morphology, selected microbial populations, volatile fatty acid (VFA) concentrations and the immune status of the weaned pig. A total of 28 piglets (24 days of age, 9.1 kg (± s.d. 0.80) live weight) were assigned to one of four dietary treatments for 8 days and then sacrificed. The treatments were (1) control diet (0 ppm COS), (2) control diet plus 5 to 10 kDa COS, (3) control diet plus 10 to 50 kDa COS and (4) control diet plus 50 to 100 kDa COS. The COS was included in dietary treatments at a rate of 250 mg/kg. Tissue samples were taken from the duodenum, jejunum and ileum for morphological measurements. Digesta samples were taken from the proximal colon to measure lactobacilli and Escherichia coli populations and digesta samples were taken from the caecum and proximal colon for VFA analysis. Gene expression levels for specific cytokines were investigated in colonic tissue of the pig. Supplementation of different MW of COS had no significant effect on pig performance during the post-weaning period (days 0 to 8; P > 0.05). The inclusion of COS at all MW in the diet significantly reduced faecal scores compared with the control treatment (P < 0.01). Pigs fed the 10 to 50 kDa COS had a higher villous height (P < 0.05) and villous height : crypt depth ratio (P < 0.05) in the duodenum and the jejunum compared with the control treatment. Pigs fed the 5 to 10 kDa COS had a lower lactobacilli population (P < 0.05) and E. coli population (P < 0.05) in the colon compared with the control group. Pigs offered the 5 to 10 kDa COS had significantly lower levels of acetic acid and valeric acid compared with the control group (P < 0.05). The inclusion of different MW of COS had no significant effect on the expression of the cytokines tumour necrosis factor-α, Interleukin (IL)-6, IL-8 and IL-10 in the gastro-intestinal tract of the weaned pig. The current results indicate that a lower MW of 5 to 10 kDa COS possessed an antibacterial activity, while the higher MW of 10 to 50 kDa was optimum for enhancing the intestinal structure.