The effects of feeding diets containing grains naturally contaminated with Fusarium mycotoxins on intestinal histology were studied in chickens raised to 10 wk of age in the absence or presence of coccidial challenge. Experimental diets included the following: controls, diets containing grains naturally contaminated with Fusarium mycotoxins, and diets containing contaminated grains 0.2% polymeric glucomannan mycotoxin adsorbent. Contaminated diets contained up to 3.8 µg/g deoxynivalenol (DON), 0.3 µg/g 15-acetyl DON, and 0.2 µg/g zearalenone. An optimized mixture (inducing lesions without mortality) of Eimeria acervulina, Eimeria maxima, and Eimeria tenella was used to challenge birds at 8 wk of age. Intestinal tissues were collected from duodenum, jejunum, and ileum prior to challenge; at the end of the challenge period (7 days postinfection; PI); and at the end of the recovery period (14 days PI). Mean villus height (VH) in the duodenum of birds fed the contaminated diets in the absence of coccidial challenge was significantly lower than that of the controls. Mean VH in the jejunum and ileum of the same birds was significantly higher compared to controls, indicating a compensatory mechanism. Fusarium mycotoxins retarded duodenal recovery from coccidial lesions, as indicated by lower duodenal VH and apparent villus surface area comparing challenged birds fed the contaminated diets to challenged controls of the same age. Increased VH was frequently associated with cryptal hyperplasia and increased numbers of mitotic figures in crypts. It was concluded that diets contaminated with Fusarium mycotoxins below levels that negatively affect performance could alter intestinal morphology and interfere with intestinal recovery from an enteric coccidial infection.