Objective To explore the correlation of Gli1 expression with clinical characteristics and prognosis of liver cancer. Methods Such Databases as PubMed, Embase, CNKI, Wanfang Database and Chinese Biomedical Literature Database were searched to collect cohort studies, which has published on the correlation between the expression of Gli1 and the clinical pathologic features of liver cancer and its prognostic value from the establishment of the databases to December 2016. Results Twelve studies with a total of 831 patients were included in this study. The high expression of Gli1 was associated with the tumor diameter >5 cm [relative risk (RR)=1.39, 95% confidence interval (CI) (1.08, 1.79)], clinical stage [RR=1.26, 95%CI (1.05, 1.51)], intrahepatic metastasis [RR=1.39, 95%CI (1.06, 1.83)] and venous invasion [RR=1.44, 95%CI (1.01, 2.04)], but the correlation of Gli1 expression was not significant with gender, histological differentiation, tumor diameter >3 cm, hepatitis B virus, cirrhosis and alpha fetoprotein. Meanwhile, the results of Meta-analysis showed that the higher Gli1 expression in liver cancer patients had a worse 3-/5-year overall survival rate and overall survival rate than those of the lower Gli1 expression group [3-year, RR=3.38, 95%CI (2.01, 5.67); 5-year, RR=1.51, 95%CI (1.19, 1.91); overall survival, RR=1.60, 95%CI (1.11, 2.30)]. And the higher Gli1 expression in liver cancer patients had a worse disease free survival rate than that in the lower Gli1 expression group [RR=1.89, 95%CI (1.35, 2.66)]. Conclusion The high expression of Gli1 is associated with poor prognostic outcome in liver cancer, and may be used as an important prognostic marker for patients with liver cancer.