OBJECTIVES: To evaluate the costs associated with the treatment of Hepatitis C Virus (HCV) treated with Peg-interferon Alpha-2a versus Peg-Interferon Alpha 2b. METHODS: For an initial distribution of patients it was used as an assumption that 60% of patients had chronic hepatitis and the other had compensated hepatitis. With this information was developed a Markov model with probabilities of disease evolution. The stages for this model from this were: liver cancer, ascites, refractory ascites, gastrointestinal bleeding, hepatic encephalopathy, liver transplantation and death. Costs are expressed in US dollars. RESULTS: The highest response rates were found with Peg-Interferon Alpha-2a for genotypes 1, 2 and 3 with a difference up to 15% compared to Peg-Interferon Alpha-2b. Due to a higher sustained virological response rate with Peg-Interferon Alpha-2a, the percentage of patients using this treatment had a lower probability of falling and developing chronic complications of the disease. Therefore, the cost of the disease treatment decreases. Also the cost of treatment with Peg-Interferon Alpha-2a is lower compared to Peg-Interferon Alpha 2b. For a 10-year projection which simulates through a Markov model that patients that did not respond to treatment evolved to chronicity of the disease costs per patient with Peg-interferon Alpha-2a was $ 25,913, while with Peg-Interferon Alpha-2b was $ 37,352, generating savings of $ 11,439 per patient who was treated with Peg-interferon Alpha-2a. CONCLUSIONS: The use of Peg-Interferon Alpha-2a was the dominant alternative because it was the most effective and least costly to treat HCV.