Background Toll-like receptors (TLRs) are important molecules for both innate and adaptive immune responses. The prevalence of TLRs polymorphism varies in different populations and controversial results were reported in HCV patients. We aimed to assess the frequency of TLR2 Arg753Gln, TLR4 Asp294Gly and TLR4 Thr399Ile polymorphisms among Egyptian children with chronic HCV and to study their relation to clinical data. Methods An observational case control study was conducted in Mansoura University Children’s Hospital, Egypt and included 100 Chronic HCV patients (63% males) with mean age of 13 ± 2.8 years in addition to 100 healthy matched controls. Diagnosis of patients relied upon persistently positive HCV PCR for at least 6 months. Eighty two patients received combined pegylated interferon α2b 60 mcg/m 2 /w and ribavirin 15 mg/kg/d. Treatment was continued for 48 weeks for responders (49 patients). All subjects were exposed to history, examination, liver functions, viral markers, HCV PCR and abdominal ultrasound. Liver biopsy was done only for patients. Gene polymorphisms were assessed by restriction fragment length polymorphism. Results Neither patients nor controls had TLR2 Arg753Gln or TLR4 Asp299Gly polymorphisms. Only 3 patients (3%) were heterozygous for TLR4 Thr399Ile polymorphism without significant difference between patients and controls (p = 0.24). No significant correlation was observed between TLR4 Thr399Ile polymorphism and viral load, histologic activity, grade of fibrosis or treatment response (p = 0.96, 0.21, 0.46, 0.49 respectively). Conclusion TLR2 Arg753Gln, TLR4 Asp294Gly and TLR4 Thr399Ile polymorphisms seem to be absent or rare and probably have no role in HCV among Egyptian population.