DiGeorge Syndrome type I (DiGSI), also known as velo-cardio-facial syndrome or 22q11.2 deletion syndrome is affecting genes involved in formation of 3rd and 4th brachial arches and causes different malformations like cardiac abnormalities, hypo- or aplasia of thymus, palate abnormalities, hypoparathyroidism, autism etc. In Most frequently it is caused by de novo deletion, in rare cases it is inherited from one of the parents. Anyway, it heavily affects persons quality of life and should be diagnosed as soon as possible. One of the obstacles in DiGSI diagnostics is deletion polymorphism – deletion can be quite of different length and involve different genes, changing patients personal prognosis in dependence of genes involved. Previously, we proposed a method, based on gene copy number quantification based on TaqMan qPCR quantification of genes of interest. However, this proposition has its limitations, which includes limited scalability (modern qPCR machines support only up to 6 channels of fluorescence per well, one target per fluorescence channel) and dependence on different qPCR machines resolution by Ct and sensitivity. Now we propose highly-multiplexed method for DiGSI testing based on QF-PCR using FAM channel for internal controls, VIC/HEX channel for regions of interest and LIZ channel for size marker. QF-PCR method advantage is possibility of use of multiple targets on single fluorescence channel by its size and spatial separation. This method is highly-sensitive, fast and highly-accurate mode of DiGSI diagnostics with possibility of making prognosis of disease severity and features. It also includes optimized protocol and run parameters for capillary electrophoresis machines. Unlike our previous method, this one can scan region of interest for multiple genes deletions without need for further precization and verification.