Aims: To evaluate practice patterns in the management of cow’s milk protein allergy (CMPA) and associated economic burden of disease on health service in Turkey.Materials and methods: This study was based on experts’ views on the practice patterns in management of CMPA manifesting with either proctocolitis or eczema symptoms and, thereby, aimed to estimate economic burden of CMPA. Practice patterns were determined via patient flow charts developed by experts using the modified Delphi method for CMPA presented with proctocolitis and eczema. Per patient total 2-year direct medical costs were calculated, including cost items of physician visits, laboratory tests, and treatment.Results: According to the consensus opinion of experts, 2-year total direct medical cost from a payer perspective and societal perspective was calculated to be $US2,116.05 and $US2,435.84, respectively, in an infant with CMPA presenting with proctocolitis symptoms, and $US4,001.65 and $US4,828.90, respectively, in an infant with CMPA presenting with eczema symptoms. Clinical nutrition was the primary cost driver that accounted for 89–92% of 2-year total direct medical costs, while the highest total direct medical cost estimated from a payer perspective and societal perspective was noted for the management of an exclusively formula-fed infant presenting either with proctocolitis ($US3,743.85 and $US4,025.63, respectively) or eczema ($US6,854.10 and $US7,917.30, respectively). The first line use of amino acid based formula (AAF) was associated with total direct cost increment $US1,848.08 and $US3,444.52 in the case of proctocolitis and eczema, respectively.Limitations: Certain limitations to this study should be considered. First, being focused only on direct costs, the lack of data on indirect costs or intangible costs of illness seems to be a major limitation of the present study, which likely results in a downward bias in the estimates of the economic cost of CMPA. Second, given the limited number of studies concerning epidemiology and practice patterns in CMPA in Turkey, use of expert clinical opinion of the panel members rather than real-life data on practice patterns that were used to identify direct medical costs might raise a concern with the validity and reliability of the data. Also, while this was a three-step study with six experts included in the first stage (developing local guidelines for diagnosis, treatment, and follow-up of infants with CMPA in Turkey) and 410 pediatricians included in the second stage (a cross-sectional questionnaire-survey to determine pediatricians’ awareness and practice of CMPA in infants and children), only four members were included in the present Delphi panel, which allows a limited discussion. Third, lack of sensitivity analyses and exclusion of indirect costs and costs related to alterations in quality of life, behavior of infants, and general well-being of infants and their parents from the cost-analysis seems to be another limitation that may have caused under-estimation of relative cost-effectiveness of the formulae. Fourth, calculation of costs per local guidelines rather than real-life practice patterns is another limitation that, otherwise, would extend the knowledge achieved in the current study. Notwithstanding these limitations, the present expert panel provided practice patterns in the management of CMPA and an estimate of the associated costs, depending on the symptom profile at initial admission for the first time in Turkey.Conclusions: In conclusion, in providing the first health economic data on CMPA in Turkey, the findings revealed that CMPA imposes a substantial burden on the Turkish healthcare system from both a payer perspective and societal perspective, and indicated clinical nutrition as a primary cost driver. Management of infants presenting with eczema, exclusively formula-fed infants, and first line use of AAF were associated with higher estimates for 2-year direct medical costs.