Alcohol intoxication at the time of burn injury exacerbates post-burn pathogenesis. Recent findings suggest gut barrier integrity is compromised after combined alcohol and burn insult, which could contribute to these complications. Tight junction proteins and mucins play critical roles in keeping the gut barrier intact. Therefore, the goal of this study was to examine the effects of alcohol and burn injury on claudin and mucin expression in the intestines. We also evaluated if the combined insult differentially influences their expression in the small and large intestines. Male C57BL/6 mice were given a single dose of 2.9g/kg ethanol prior to a ~12.5% body area burn. One and three days following injury, we profiled expression of several tight junction proteins, mucin, and bacterial 16S rRNA genes in small and large intestine using qPCR. We observed >50% decrease in claudin-4 and claudin-8 genes in both ileal and colonic epithelial cells one day after injury. Claudin-2 was significantly upregulated, and occludin was down-regulated in small intestine one day following injury. Mucin-3 expression was substantially elevated (>50%) in small intestine, whereas mucin-2, and mucin-4 were considerably diminished in the colon (>50%) one day following injury. Most parameters were normalized to sham levels on day three, except for mucin-3 and claudin-8, which remained decreased in large intestine. Neither alcohol nor burn alone resulted in changes in junction or mucin gene expression compared to shams. This was accompanied with increases in the family of Gram-negative bacteria, Enterobacteriaceae, in both small and large intestine one day following injury. These findings suggest that alcohol and burn injury disrupts normal gut microbiota and alters tight junction and mucin expression in the small and large intestines.