The identification of associations between IL28B variants and spontaneous clearance of hepatitis C virus (HCV) raises the issues of causality and of the net contribution of host genetics to the trait. To estimate more precisely the net effect of IL28B genetic variation on HCV clearance, we optimized genotyping and compared the host contribution in a multiple and a single source cohort to control for viral and demographic effects. The analysis included individuals with chronic or spontaneously cleared HCV infection from a multiple (n=389), and from a single source cohort (n=71). We performed detailed genotyping in the coding region of IL28B and searched for copy number variation to identify the genetic variant or haplotype carrying the strongest association with viral clearance. This analysis was used to compare the effect of IL28B variation in both cohorts. Haplotypes characterized by carriage of the major alleles at IL28B single nucleotide polymorphisms (SNPs) were highly overrepresented in individuals with spontaneous clearance compared to those with chronic HCV infection (66.1% versus 38.6%, P=6*10(-9) ). The Odds Ratio for clearance was 2.1 (CI(95) 1.6-3.0) and 3.9 (CI(95) 1.5-10.2) in multiple and single source cohort, respectively. Protective haplotypes were in perfect linkage (r(2) =1.0) with a non-synonymous coding variant (rs8103142). Copy number variants were not detected. CONCLUSIONS: We identified IL28B haplotypes highly predictive of spontaneous HCV clearance. The high linkage disequilibrium between IL28B SNPs indicates that association studies need to be complemented by functional experiments to identify single causal variant(s). The point estimate for the genetic effect was higher in the single source cohort, which effectively controls for viral diversity, gender and co-infections and therefore offers a precise estimate of the net host genetic contribution. (HEPATOLOGY 2011.).