We measured hepatitis C virus (HCV) RNA and antibodies against HCV recombinant proteins (C22/S1, E1/S2, E2/NS1, C33/NS3, C100/NS4, NS5) in serial serum samples from 22 interferon-treated patients with a long-term follow up (range: 36–44 months). Eleven of them showed persistently normal liver function tests and a significant histological amelioration or a complete resolution of chronic hepatitis (long-term responders, LTRs). In the remaining 11 patients (non-responders (NRs)) liver function tests normalized temporarily during therapy or remained unchanged. At the end of the follow up (3 years), viraemia was undetectable in six of 11 LTRs (54.6%). HCV-RNA was always detectable in the serum of NRs (p = 0.017). At admission, anti-C22/S1, anti-E1/S2, anti-E2/NS1, anti-C33/NS3, anti-C100/NS4 and anti-NS5 were detected in 95.4%, 40.9%, 77.3%, 95.4%, 72.7%, and 77.3% of the patients, respectively. Three years after suspension of therapy, anti-C100/NS4 was undetectable in five of six (83.3%) LTRs who cleared HCV-RNA and in only one with ongoing viraemia (20%). Anti-E2/NS1 was undetectable in 54.5% of LTRs and in no NRs (p = 0.067). Anti-E1/S2 was detected more frequently in LTRs than in NRs (81.8% vs 45.5%). Serum levels of anti-C22/S1, C33/NS3 and NS5 did not change during therapy and the follow up in either group of patients. The clearance of viraemia in LTRs was associated with that of anti-C100/NS4 (p = 0.017). Serum HCV-RNA and anti-C100/NS4 appear suitable tools for monitoring patients who respond to therapy. More than 40%) of LTRs remained HCV-RNA-positive in spite of the biochemical remission of their liver diseases.