This study was performed to investigate the effect of feeding
Brassica
spp. including full-fat rapeseed, canola meal, and allyl isothiocyanate (
AITC
) to broiler chicken challenged with
E. maxima
. A total of 576 one-day old male broiler chicks were completely randomized to 8 treatments with 6 replicated cages and 12 birds per cage. The treatment diets consisted of nonchallenge control (
NC
, corn-SBM based diet), challenge control (
CC
), 10% rapeseed (10RS), 30% rapeseed (30RS), 20% canola (20CLM), 40% canola (40CLM), 500 ppm AITC (500AITC), and 1,000 ppm AITC (1000AITC). At d 14, all birds were challenged, except NC group, with a subclinical dose of
E. maxima
. Intestinal permeability was conducted on 5 d post-infection (
dpi
) and for oocyst shedding 5 to 6 dpi feces were pooled and collected. On 6 dpi, growth performance, lesion score, histomorphology, and gene expression were measured. The growth performance result showed that 10RS and 30RS groups had lower BW, BWG, FI, and higher FCR (
P
< 0.0001). During the challenge and overall periods, NC group had highest BW, BWG, and FI, and lowest FCR. The inclusion of canola meal showed lower performance during prechallenge period but was able to catch up BWG during challenge period. The AITC levels showed similar growth performance to CC group. Intestinal permeability for 20CLM, 40CLM, 500AITC and 1000AITC was similar to NC group, whereas CC, 10RS, and 30RS had higher permeability compared to NC (
P
< 0.0001). Oocyst shedding was significantly lower for 40CLM and NC, whereas all other treatments had higher oocyst shedding (
P
< 0.0001). All the challenged treatment groups had higher lesion score and microscore than NC (
P
< 0.0001). Histomorphology data showed that jejunum villus height (
VH
) for 1000AITC was similar to NC group, whereas CC group had the lowest VH (
P
= 0.01). The 30RS group had lower VH: crypt depth (
CD
) ratio in the jejunum and ileum. The gene expression at 6 dpi for claudin1, occludin, IL2, IL6, GLUT5, EAAT, B
o
AT, and LAT1 was significantly changed among the treatments. The results suggest that 30RS retards growth performance and deteriorate gut health during coccidiosis and should not be fed to chicken during the starter phase. Canola meal showed decline in growth prechallenge but maintained growth and intestinal health during the challenge period at 40% inclusion. AITC at 1,000 ppm showed similar growth as control group, but with improved gut health during the challenge period. Canola meal could be a good alternative to SBM especially during coccidiosis, whereas AITC needs to be tested vigorously in animal feeding regime.