Abstract Background The role of estrogen receptor alpha (ERa), estrogen receptor beta (ERb) and ERa36 signaling in hepatocellular carcinoma (HCC) is not fully addressed. Methods In this study, three cohorts were included: (i) primary HCC patients ( N = 76, cohort P), (ii) colorectal liver metastasis (mCRC) ( N = 32, cohort S), and (iii) HCC from The Cancer Genome Atlas (TCGA) ( N = 121). The levels of ERa36 and wtER36 were measured and their correlation with clinicopathologic features was determined. Results WtERa was downregulated and that ERa36 was upregulated in tumor tissues in both cohort P and TCGA data set. ERa36 was downregulated in tumor tissues in cohort S. In cohort P, wtERa was differentially expressed in gender ( P