Hepatitis C virus genotypes and subtypes determination is an important factor for understanding the epidemiology of the virus, in the pre-treatment evaluation of the patients and in defining better treatment strategies. In the present study, we compared two commercially available assays for HCV genotyping: the reverse hybridization based Innogenetics INNO-LiPA HCV II and the direct sequencing by TRUGENE assay. The study included 31 HCV-RNA positive Egyptian patients; 18 patients with chronic active hepatitis, 8 with HCC, and 5 with cirrhosis. Using the TRUGENE genotyping test, all the samples had genotype 4 (100%) and subtyped as 4a in 18/31(58%), 4c in 10/31 (32%), 4e in 1/31 (3%), 4a/c in 1/31 (3%), and 4g in 1/31 (3%). Using the INNO-LiPA assay, 30 samples had genotype 4 (97%), and 1 sample had genotype 1e (3%). One sample showed mixed infection with type 4f and type 1. Only six samples were subtypable by INNO-LiPA, three were genotype 4c/d, and the other three were 4f, 4e, and 1e. Seven samples gave reactivity in the INNO-LiPA of lines 5, 6, 16, 17, 18, which are considered untypable by the interpretation chart but considered to be a rare HCV genotype 4 by the manufacturer. At the genotype level, there was a 97% concordance between TRUGENE sequencing and INNO-LiPA, but at the subtype level the concordance rate was 3% only. We conclude that the TRUGENE genotyping assay is a reliable test for HCV genotyping for the detection of major types and subtypes detection, while INNO-LiPA is a good test at the genotype level but unreliable for subtyping especially in the Egyptian population. This is mainly due to the high diversity of genotype 4, which is the most prevalent genotype in Egypt.