<div><p>Background</p><p>Defects of autophagy and endoplasmic reticulum (ER) stress are related to many diseases and tumors. However, only a few studies have examined hepatocellular carcinoma (HCC) as related to these processes. Therefore, in this study, we investigated the expression and extent of autophagy and ER stress-related markers in HCC and their influence on clinical characteristics and prognosis for each protein.</p> <p>Methodology</p><p>The expression of autophagy-related markers (LC3 and Beclin-1) and ER stress-related markers (GRP78 and CHOP) was analyzed by immunohistochemistry on tissues from completely resected specimens of 190 HCC patients. Their influence on clinicopathologic features and prognosis were evaluated using the chi-square test and Kaplan-Meier analysis. Correlations of each protein were determined by Spearman's correlation analysis. </p> <p>Principal Findings</p><p>LC3 expression was not correlated with TNM, BCLC stage, or Edmonson-Steiner grading, whereas it was correlated with longer overall survival (OS) (<i>p</i> = 0.039) and tended to be related with longer time to recurrence (TTR) (<i>p</i>=0.068) although it did not show statistical significance. Multivariate analysis indicated that LC3 expression was a significantly independent prognostic factor of OS (HR, 0.42; 95% CI, 0.22-0.80; <i>p</i>-value=0.009) and TTR (HR, 0.54; 95% CI, 0.33–0.90; <i>p</i>=0.017). Expression of LC3 in advanced stages of TNM (III) (<i>p</i>=0.045) and Edmonson-Steiner Grades (III and IV) (<i>p</i>=0.043) was correlated with longer survival, but not in the early stages. A positive correlation was not observed between the expression of autophagy-related markers and ER stress-related markers.</p> <p>Conclusion</p><p>Our results suggest that the expression and extent of LC3 might be a strong prognostic factor of HCC, especially in patients with surgical resection.</p> </div