The glycosylphosphatidylinositol (GPI) anchor is a glycolipid with one function: teth-ering proteins to the cell surface. Synthesis and remodeling of the GPI anchor and linkage of proteins are highly conserved processes in a magnitude of species. About 10% of all surface proteins are anchored via the GPI moiety on all cells of the human body. GPI-APs (GPI anchored proteins) play important roles in a high variety of vital processes from embryogenesis over immune system regulation to neuronal function. Consequently, deficiencies in the pathway of GPI anchor biosynthesis have essential implications in life, as more than 200 individuals with disease-causing mutations in 21 of the genes of the GPI anchor biosynthesis pathway have been described in the literature. Despite the advances in next generation sequencing (NGS) technology, the assess-ment of exome or genome data of individuals with suspected biosynthesis defects of the GPI anchor (GPIBDs) remains challenging due to the broad phenotypic spectrum. During my thesis I contributed to the publication of over 29 cases that were diag-nosed with advanced phenotyping approaches for GPIBDs in NGS, flow cytometry, and computer-assisted facial image analysis. The narrative of the three articles about congenital GPIBDs follows an improvement of diagnostic methods: First, the development of NGS based techniques that enabled the identification of non-coding mutations in PGAP3 in clinically well characterized cases of HPMRS4. Second, I used a standardized flow cytometry analysis on fibro-blasts, permitting functional validation of inherited pathogenic mutations in PIGG. Third, the application of automated facial analysis as proof of principle for a disorder specific facial gestalt in congenital GPIBDs as a pathway disorder. In the fourth arti-cle, I present results of a novel disease entity in an acquired GPIBD and methods for its clinical diagnostics. Conclusively, the completion of this thesis returned advanced methods that im-proved the diagnostic yield of GPIBDs and can also be transferred to other rare monogenic disorders.