The impact of two different strains of Clostridium perfringens (Cp) (NE-18 and NE-36) on mRNA expression of genes encoding proteins involved in cell apoptosis, intestinal tight junction and production of immunoglobulins and mucin in broiler chickens was investigated. A total of 468 male Ross 308 broilers was assigned to a 2 x 3 factorial arrangement of treatments. Factors were antibiotics (+/-), necrotic enteritis (NE) and challenge (-/ NE-18/ NE-36). A significant interaction between antibiotic treatment and challenge was observed on the expression of gene CASP3 (P < 0.05); NE-18 upregulated CASP3 only in the presence of antibiotics, while NE-36 upregulated this gene regardless of antibiotic supplementation. Interestingly, both NE strains upregulated CASP8 compared to the control treatment, but NE-36 showed higher CASP8 expression than observed with the NE-18 treatment (P < 0.001). It was shown that challenge significantly downregulated OCLD (P < 0.001), ZO-1 (P < 0.05) and MUC2 (P < 0.001). CLDN1 was significantly upregulated (P < 0.001) by both the NE-36 and NE-18 challenge, but NE-36 showing comparatively greater effects compared to NE-18. A significant antibiotic × challenge interaction on MUC5ac was observed (P < 0.05), where both NE- 18 and NE-36 upregulated MUS5ac when antibiotics was applied, but only NE-36 showed such upregulation in the absence of antibiotics. IgG and IgM were significantly downregulated (P < 0.001) by both strains of Cp. These results indicate that NE challenge alters the expression of genes investigated and different strains of Cp have varying impacts, which has a direct impact on severity of the disease.