The variations across the country in the methodological reporting of Atrial Septal Defect (ASD), one type of birth defect, would suggest misleading gaps in reported prevalence rates. Using the data in 2012, we executed Poisson regression analysis to examine the association of prevalence rates of ASD with coding systems adjusting for the potential confounding factors. We found a two-fold higher prevalence rate of ASD for states using ICD-9-CM without exclusion PFO, compared to those using the coding system of the CDC or ICD-9-CM with exclusion PFO for case definition. Furthermore, an interaction term between coding system and case ascertainment methods were also observed. The study revealed that coding systems and case ascertainment methods may lead highly varied prevalence rates of ASD across States A standardized criteria to bridge this variability will play an important role in public health polices and prevention programs.