This study aimed to evaluate the effect of yacon (Smallanthus sonchifolius) flour and copaiba oil on the productive performance and intestinal integrity in broilers from 1 to 21 days of age which were challenged with Eimeria on day 14. One-day old Cobb 500 male chicks (n=120) were randomly distributed into four groups, using three replicates and 10 birds per replicate. The treatments were: T1, basal diet without coccidiostat (negative control); T2, basal diet containing coccidiostat (positive control); T3, as T1 + yacon flour (0.25%); T4, as T1 + copaiba oil (0.15 ml/kg). Six birds were slaughtered at the end of the trial and gut samples were collected to measure villus height, crypt depth, number of caliciform cells and the rate villus height/crypt depth. Also, the number of oocysts/g of faeces was evaluated. No significant differences were found between treatments on body weight gain, feed intake and feed conversion. In addition, no significant difference was found on villus height. Chicks treated with copaiba oil (T4) showed larger crypt depth in duodenum and lowest number of calciform cells in ileum (p<0.05). No statistical difference was found in relation to oocyst counts. Supplementation with copaiba oil showed positive effects on cellular regeneration in the intestine in chickens experimentally infected with Eimeria.