Although replicons have been used to demonstrate hepatitis C virus (HCV) inhibition by alpha interferon (IFN-␣), the detailed inhibition kinetics required to mathematically model HCV RNA decline have been lacking. Therefore, we measured genotype 1b subgenomic replicon (sg1b) RNA levels under various IFN-␣ concentrations to assess the inhibition kinetics of intracellular HCV RNA. During nine days of IFN-␣ treatment, sg1b RNA decreased in a biphasic, dose-dependent manner. Using frequent measurements to dissect these phases during IFN-␣ treatments of 100 and 250 U/ml revealed that the first-phase sg1b RNA decline began ϳ12 h posttreatment, continued for 2 to 4 days, and then exhibited a distinct flat or slower second phase. Based on these data, we developed a mathematical model of IFN-␣-induced intracellular sg1b RNA decline, and we show that the mechanism(s) mediating IFN-␣ inhibition of HCV acts primarily by reducing sg1b RNA amplification, with an additional effect on HCV RNA stability/degradation detectable at a dose of 250 U/ml IFN-␣. While the extremely slow or flat second phase of viral RNA inhibition observed in vitro, in which there is little or no cell death, supports the in vivo modeling prediction that the more profound second-phase decline observed in IFN-␣-treated patients reflects immune-mediated death/loss of productively infected cells, the second-phase decline in viral RNA with a dose of 250 U/ml IFN-␣ suggests that a further inhibition of intracellular HCV RNA levels may contribute as well. As such, dissection of HCV IFN-␣ inhibition kinetics in vitro has brought us closer to understanding the mechanism(s) by which IFN-␣ may be inhibiting HCV in vivo.Hepatitis C virus (HCV) is remarkably efficient at establishing persistent infection, affecting approximately 200 million persons worldwide of whom 20% to 30% will likely progress to cirrhosis (17). However, the current treatment option of alpha interferon (IFN-␣) in combination with ribavirin is ineffective in eliminating the virus in a large proportion of chronic hepatitis C patients (8, 13). Hence, there is a compelling need to better understand HCV infection and the dynamics of HCV inhibition achieved under antiviral therapy in order to optimize the use of IFN-␣ and ribavirin as well as new agents that are in development.Over the last decade, clinical studies that included frequent serum sampling during treatment with IFN-␣ have afforded a detailed description of the extracellular viral RNA inhibition kinetics achieved in patients and thus have provided insights into HCV infection dynamics and treatment outcomes (7, 22). Specifically, it has been shown that during chronic HCV infection in the absence of therapy, the level of serum HCV RNA does not vary significantly (Ͻ0.5 log) on time scales of weeks to months (18). However, when chronically infected patients are treated with IFN-␣ alone or IFN-␣ plus ribavirin, HCV RNA typically declines in a biphasic pattern. The first rapid-phase decline, which begins 8 to 10 h after IFN-␣ administration, las...