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Aim: To demonstrate the effect of the Syrian refugee population on the prevalence of congenital TORCH (Toxoplasmosis, Other [syphilis, varicella‐zoster, 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. [ABSTRACT FROM AUTHOR]