Objective To identify the sex-related DNA copy number alterations(CNA) in hepatocellular carcinoma(HCC). MethodsHigh-resolution array comparative genomic hybridization(array-CGH) was used to examine 17 female and 46 male HCCs. Two-tailed Fisher’s exact test or χ2 test was used to compare the differences in CNA between females and males. ResultsThe overall frequencies and patterns of CNA in female and male cases were similar. However, female HCC tumors presented more copy number gains compared to male on 1q21.3-q22(76.5% vs 37.0%, P=0.009), 11q11(35.3% vs 0.0%, P=0.000 2) and 19q13.31-q13.32(23.5% vs 0.0%, P=0.004), and more loss on 16p11.2(35.3% vs 6.5%, P=0.009). Relative to females, male cases had more copy number loss on 11q11(63.0% vs 17.6%, P=0.002). Further analyses showed that 11q11 gain was correlated with 19q13.31-q13.32 gain(P=0.042) and 16p11.2 loss(P=0.033), while 1q21.3-q22 gain was correlated with 19q13.31-q13.32 gain(P=0.046). ConclusionOur findings suggest that CNA may play an important role in sex-related difference in HCC development.