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• PD-1/PD-L1 signalling involves T-cell exhaustion in patients with chronic hepatitis B virus (HBV) infection. • Increased expression of PD-1 is considered to be associated with infectious diseases. • PD-1.9 and PD-1.9 are associated with HBV-associated liver disease outcomes. • Increased sPD-1 levels are associated with HBV-related liver inflammation and fibrosis. Programmed cell death-1 (PD-1) variants and circulating level of soluble PD-1 are associated with susceptibility to malignant and infectious disease. This study aimed to examine the association of PD-1.5 and PD-1.9 variants, and plasma sPD-1 level with hepatitis B virus (HBV) infection and disease progression. The study cohort consisted of adults infected with HBV (n =513) – stratified by clinical course, including chronic hepatitis B (CHB, n =173), liver cirrhosis (LC, n =134) and hepatocellular carcinoma (HCC, n =206) – and matched healthy controls (HC, n =196). The PD-1.5 (rs2227981 C/T) and PD-1.9 (rs2227982 C/T) genetic variants were genotyped by Sanger sequencing, and plasma sPD-1 levels were quantified by enzyme immunoassay. Plasma sPD-1 levels were significantly higher among patients infected with HBV. The highest plasma sPD-1 levels were observed in patients with CHB, followed by patients with LC and HCC. In addition, the plasma sPD-1 levels correlated positively with liver inflammation [aspartate transaminase (AST): rho=0.57, P <0.0001; alanine aminotransferase: rho=0.57, P <0.0001], and were positively correlated with liver fibrosis [AST to platelet ratio index score: rho=0.53, P <0.0001). The PD-1.9 TT genotype was less common in patients with CHB compared with patients with LC, HCC, and HCC+LC in both codominant and recessive models (P <0.01), and was found to be a risk factor for HCC predisposition {HCC vs non-HCC: odds ratio (OR) 2.0 [95% confidence interval (CI) 1.13–3.7], P adj =0.017}. The PD-1.5 CT genotype was associated with reduced risk of acquiring HCC [OR 0.6 (95% CI 0.4–0.9), P adj =0.031]. sPD-1 level was associated with liver inflammation and progression of liver fibrosis, and the PD-1.5 and PD-1.9 variants were associated with HBV infection and progression of liver disease. [ABSTRACT FROM AUTHOR]