Pectus excavatum (PE) is the most common deformity among anterior chest wall abnormalities. Although many theories on the pathogenesis of PE have been described, the uncertainty is still going on whether it is a result of developmental, biochemical, or biomechanical reasons or their combination. The aim of this study was to evaluate the biochemical parameters that may cause or be associated with the development of PE between children with PE and their healthy peers. A total of 33 patients' medical records were retrospectively analyzed who followed up because of pectus excavatum between 2019 and 2021. A control group was formed from 32 healthy children from the hospital records with similar age and gender profiles as the patient group. The data from both groups were collected and statistically analyzed in terms of gender, age, and laboratory tests, including hemogram, Vit B12, Parathormone (PTH), Vit.D, Alkaline phosphatase (ALP), and serum Calcium (Ca) and Phosphor (P) levels. Compared to the control group, statistically, significantly higher serum ALP, P, and PTH levels with low Vit.B12 levels were detected. The significant difference in the levels of ALP, PTH, P, and Vit B12, which have an important place in the construction and development of osteochondral structures, may impair the remodeling capacity of the costosternal structure with the contribution of thoracic biomechanics. When PE deformity is noticed, if appropriate medical treatment such as vitamin and mineral supplements and diet regulation is applied to children in the follow-up process, the process can be slowed down, and the deformity can be alleviated.