Aim: To demonstrate the effect of the Syrian refugee population on the prevalence of congenital TORCH (Toxoplasmosis, Other [syphilis, parvovirus B19], Rubella, Cytomegalovirus [CMV] and Herpes) infections and to evaluate the cost-effectiveness of population-based TORCH screening during pregnancy in Turkey. Methods: Pregnant women (n = 9754) were enrolled. Ultrasonographic findings, immunoglobulin (Ig)M and IgG seropositivity, avidity, amniocentesis and DNA-polymerase chain reaction (PCR) results were compared. Costs were calculated based on invoice amounts from the Health Applications Communique pricing system. Results: The prevalence of TORCH seropositivity in Turkey was not significantly different between all regions (P > 0.05). Overall, 1333 (13.67%) pregnant Syrian refugees were included in the study. Acute CMV, rubella and Toxoplasma gondii infections (according to low IgG avidity in IgM positive patients) were detected in 17.82%, 21.53% and 14.07% of women, respectively. Twenty-four women underwent an amniocentesis procedure and nine of them had positive DNA-PCR and reverse transcription-PCR results. All women with positive results opted to terminate the pregnancy. There was no statistical difference among groups according to the rate of low IgG avidity in IgM-positive patients and termination rates for T. gondii, rubella and CMV (P > 0.05). Total cost for screening the entire study population was presented in US dollars (USD). A total of 71 529 and prenatal diagnosis with positive invasive test results were obtained in nine women: toxoplasmosis in four, CMV in three and rubella in two women. Conclusion: Population-based screening for prenatal TORCH infections is not cost-effective in Turkey. Syrian refugees have a limited effect on the increasing prevalence of congenital TORCH infections.