Background: A chronic HBsAg carrier state, a major cause of viral spread in a community, is one of the consequences of hepatitis B virus (HBV) infection. Although successful immunization programs have been initiated to eliminate the virus, there is still a large number of people with HBV infection worldwide. This study was designed to investigate the effect of indomethacin treatment on HBV markers in humans, in comparison with a control group. Methods: In total, 65 chronic 'healthy' HBV carriers were involved in the study. Patients were divided randomly into two groups. Group I (n = 42) received oral indomethacin 75 mg daily for 6 months. Group II (n = 23) acted as control. Patients in both groups were followed up for 6 months, during which laboratory tests, including viral parameters, were performed periodically. Liver biopsy was done in 17 patients (11/42 of the indomethacin group and 6/23 of the control group). Results: All liver biopsies showed grade 0-2 and stage 0-1 HBV in both groups (P > 0.05). HBsAg positivity did not change in any patient in either group. Five patients who had positive HBeAg in group I became negative 4 months later, while patients in group II continued to be positive at 6 months (P < 0.001). Similarly, all patients receiving indomethacin exhibited a total anti-HBeAg immunoglobulin response at 6 months, while the control group remained the same during this period (P < 0.05). HBV DNA, as detected by polymerase chain reaction in 20/22 (91%), was negative in group I at the end of 6 months. No change was observed in group II (P = 0.007). Conclusions: Although no biochemical analyses were performed on prostaglandins in the present study, the results suggest that the prostaglandin pathway may be involved in the pathogenesis of the immune response against HBV, and that the suppression of viral replication is achieved as indicated by the disappearance of HBeAg and HBV DNA in healthy chronic HBV carriers.