This experiment was conducted to evaluate the effect of Bacillus subtilis (BS) on broiler performance and health after intramuscular inoculation with E. coli and compare its effect with a growth promoter antibiotic. In a completely randomized design manner, 360 male Ross 308 chicks were divided into 6 treatments and 5 replicates of 12 chicks in each replicate. Experimental treatments included control diet, control + E. coli (0.5 mL of culture containing 108 CFU of E. coli/ml), control + 0.1% BS, control + 0.05% bacitracin methylene disalicylate (BMD), control + E. coli and BS, and control + E. coli and BMD in a factorial arrangement (3 × 2). Addition of BMD or BS to the control diet significantly (P < 0.01) increased body weight and decreased FCR, but E. coli challenge adversely reduced (P < 0.01) body weight and increased FCR, so that the addition of BMD or BS did not compensate growth reduction. E. coli challenged chicks had the lowest vaccine titers for ND, IB, AI, and IBD and the highest were observed in chicks fed BS. The E. coli challenge significantly (P < 0.01) increased albumin, globulin, cholesterol, triglyceride, LDL, ALT, and ALP indices. Addition of BMD and BS decreased albumin and globulin in challenged chick's plasma but had no effect on plasma lipid profile concentration. The E. coli challenge decreased villus height and increased crypt depth and goblet cell numbers significantly (P < 0.01). In birds subjected to BMD or BS, crypt depth decreased and villus height increased (P < 0.01), compared with the control diet. Challenge of E. coli significantly (P < 0.01) increased the bacterial population of E. coli, coliforms, and Salmonella in cecal parts of broilers' intestines. In challenged birds receiving BMD or BS, E. coli, coliform, and Salmonella populations of ceca showed a significant (P < 0.01) reduction. Both BMD and BS increased the digestibility of nutrients significantly (P < 0.01), but a reduction was observed in E. coli challenged groups. Results of the study suggest that spore-forming probiotics are partially effective in unsuitable rearing situations such as colibacillosis in which the load of harmful bacteria is high.