OBJECTIVE To investigate the liver pathological changes and the clinical features of patients with hepatitis B virus (HBV) infection in their immune tolerant phase and non-active status. METHODS Fifty-four patients with chronic HBV infection in their immune tolerant stage and another 47 patients with the same infection but in non-active status were involved in this study. Statistical analysis including the ages and sex of the patients, their serum levels of HBV DNA, hepatocytic expression of HBsAg and HBcAg and their liver pathology were studied and statistically analyzed. Histological grading of inflammation and staging of fibrosis in the livers were also compared and analysed in patients with different levels of serum ALT. RESULTS The sex ratio of the two groups was of no significant difference. The average age of the patients in the non-active status [(28.11+/-8.60) years.] was older than that of the patients in the immune tolerant stage [(24.93+/-7.21) years], showing a significant difference (P < 0.05). The serum levels of HBV DNA of the patients in the immune tolerant stage were high and 94% of them had a HBV DNA higher than 106 copies/ml. In the non-active status group, 89% of the patients were HBV DNA negative. Between the two groups of patients there were no significant differences in the histological grades of liver inflammation or in the hepatocytic expressions of HBsAg and HBcAg. The stage of fibrosis was higher in the non-active status group than in the immune tolerant stage group, showing a significant difference between these two groups (u = 2.004, P < 0.05). The fibrosis stages of the livers of patients of a higher but within normal ALT level were markedly higher than those of a lower but within normal ALT level patients (u = 3.274, P less than 0.01). CONCLUSIONS Patients infected with HBV in non-active status may have experienced some occult courses of immune active stages; they are older in age and have higher levels of fibrosis. ALT sustained at a high level but within the normal range may indicate a higher degree of fibrosis, therefore liver pathological studies should be recommended for this kind of patient.