Abstract Background A 9-month-old infant presented with developmental motor delay. Comprehensive evaluation including microarray and brain MRI revealed no specific abnormalities except for hypotonicity. The patient's perinatal history, including newborn screening test (NST), showed no remarkable findings. Additionally, the infant exhibited facial dysmorphism and microcephaly, leading to another NST to explore potential metabolic diseases. Upon NST, Thyroid-Stimulating Hormone (TSH) levels were 1.86 and 1.27 mlU/L (duplicate testing results; reference value: <12 mlU/L), 17-Hydroxyprogesterone (17-OHP) levels were 0.55 and 0.48 ng/mL (duplicate testing results; reference value adjusted for body weight: <5.0 ng/mL), and total Galactose (Gal) and Galactose-1-Phosphate (Gal-1-P) levels were 1.68 mg/dL (reference value: <8 mg/dL). Methods Upon inspection of the dried blood spot (DBS) sample, the DBS used for the tests partially appeared to be inadequately collected on the absorbent filter paper, which could cause errors related to the disc and specimen itself. Consequently, re-sampling and re-testing were necessary to ensure accuracy. A second NST was performed with the new DBS samples. In the second NST results, most parameters were within the allowable ranges. However, the TSH levels were notably below the detectable limit (<0.7 mlU/L), and the 17-OHP levels were significantly elevated at 332ng/mL, diverging markedly from the initial NST results. To ensure reliability of the measured test results, TSH levels were analyzed using both the existing PerkinElmer equipment and compared with results from a Cobas 8000 system (Roche) and mass spectrometry. Similarly, 17-OHP levels were also compared using mass spectrometry. Results Upon comparing the TSH results, both analytical methods (PerkinElmer and Roche) yielded identical outcomes. However, significant discrepancy was observed when compared to mass spectrometry results. Review of the relevant testing batches showed no significant quality control issues with the NST, leading to clinical suspicion of ethylene-diamine-tetraacetic acid (EDTA)-induced interference. According to existing literature, when NST are conducted using the lanthanide fluorescence method, distortions can occur in DBS containing EDTA, depending on the concentration of EDTA present. In such cases, the EDTA-induced interference may result in false-negative TSH and false-positive 17-OHP results. These discrepancies can be differentiated using standard MS/MS testing. With regards to our case, upon enquiry, the second DBS sample was revealed to be collected from an existing EDTA sample rather than directly from the patient. Thus, adequate DBS discs from the initial sample were obtained and re-analyzed for NST using mass spectrometry, with final results reporting no specific abnormalities. Conclusions The discrepancies observed in TSH and 17-OHP levels between the first and second set of DBS samples were found to be unrelated to other laboratory factors, such as quality control issues. Instead, they were conclusively identified as false-negative and false-positive results associated with interference due to the use of EDTA-containing collection bottles. Mass spectrometry analysis was able to confirm the interference. Clinical awareness should be promoted in order to prevent EDTA-induced interference in NST.