The aim of the present study was to investigate the effects of cytomegalovirus (CMV) infection on the prognosis of inflammatory bowel disease (IBD). Various databases were searched using a combination of keywords associated with CMV infection and IBD. Subsequent to the selection of relevant studies in line with strict inclusion and exclusion criteria, a meta-analysis was conducted using the Stata 12.0 software. A total of 195 studies were initially retrieved, including 28 studies in Chinese and 167 in English. Following the exclusion of unsuitable studies, 7 cohort studies with 374 IBD patients were included in the meta-analysis. The results of the present study identified significant differences between patients with and without CMV infection regarding the disease duration of IBD [standardized mean difference, −0.81; 95% confidence interval (CI), −1.19 to −0.43; P<0.001], the efficacy of corticosteroid therapy [relative risk (RR), 1.24; 95% CI, 1.02–1.49; P=0.029], the colectomy rate (RR, 2.13; 95% CI, 1.03–4.40; P=0.042) and the incidence of severe IBD (RR, 1.32; 95% CI, 1.04–1.67; P=0.022). Considering the IBD onset area, patients with CMV infection may have higher susceptibility to pancolitis (RR, 1.31; 95% CI; 1.01–1.72; P=0.045); however, no difference in susceptibility to left-sided IBD was observed between patients with or without CMV infection (RR, 0.97; 95% CI, 0.72–1.30; P=0.828). In conclusion, CMV infection may be associated with the disease duration, efficacy of corticosteroid therapy, colectomy rate, severe IBD incidence and disease location of IBD; thus, the presence of CMV infection may be considered as an important biomarker for determining the prognosis of IBD.