For this study, threonine (Thr) deficiency was hypothesised to exacerbate the intestinal damage induced by feed withdrawal with coccidial infection because of its high obligatory requirement by the gut; two dietary Thr treatments (0·49 and 0·90 %) were applied to chicks from 0 to 21 d of age. At 13 d of age, feed was withdrawn for 24 h from one-half of birds of each dietary treatment with subsequent gavage of a 25× dose of coccidial vaccine. Overall, there were four treatments with eight replicate cages per treatment. Under combined challenge, birds fed the Thr-deficient diet had 38 % lower 13–21-d body weight gain (P≤0·05) compared with birds fed the Thr-control diet. At 21 d, the challenged group fed low Thr had higher number of oocysts (+40 %, P=0·03) and lower crypt depth (−31 %, P<0·01). In addition, birds fed the low-Thr diet had higher gut permeability as measured after 2 h of administration of fluorescein isothiocyanate-dextran (3–5 kDa, P<0·01), which may be attributed to decreased IgA production (P=0·03) in the ileum. In caecal tonsils, the challenged group fed low Thr had lower CD3:Bu-1 ratio (P≤0·05), along with a tendency for lower CCR9 mRNA expression in birds fed the low-Thr diet (P=0·10). In addition, Thr deficiency tended to increase IL-10 mRNA expression regardless of infection (P=0·06), but did not change interferon-γ mRNA expression upon coccidial infection (P>0·05). Overall, Thr deficiency worsened the detrimental effects of combined feed withdrawal and coccidial infection on growth performance and oocyst shedding by impairing intestinal morphology, barrier function, lymphocyte profiles and their cytokine expressions.