This document details the methodology behind the Modell Database of Congenital Disorders (MGDb) and its role in estimating endogenous congenital disorders and their baseline birth prevalence using historical epidemiological studies, congenital anomaly registries, and genetic databases to inform public health policy where local data are lacking.  An overview of the terminology used, development of equations and tables to standardize estimations, intervention impacts, database outputs and data limitations is provided.