Autophagy is an evolutionarily conserved cellular process that degrades cytoplasmic materials through the lysosomal pathway. The deregulation of autophagy is associated with several diseases, particularly cancer. Hepatocellular carcinoma (HCC) is one of the most aggressive cancers with a poor prognosis. The expression of autophagy-related genes in HCC and their relationships with HCC are largely unknown. In the present study, we analyzed the expression of autophagy-related genes based on the Oncomine database and quantitative PCR of HCC and adjacent liver tissues. We found that the mRNA and protein expression of GABARAPL1 was significantly decreased in HCC tissues compared with their adjacent liver tissues. In HCC cancer cell lines, overexpression of GABARAPL1 inhibited cell growth, while knockdown of GABARAPL1 expression via siRNA promoted cell growth. In addition, we found a significant correlation of low GABARAPL1 expression with poor differentiation of HCC cells (P=0.018), and with the absence of tumor capsules (P=0.047). Kaplan-Meier survival analysis showed a significant association between low GABARAPL1 expression and poor prognosis of HCC patients (P=0.0094). Our data showed for the first time that GABARAPL1 expression is associated with poor prognosis of HCC patients.