Background: Fanconi anemia (FA) is an inherited rare disorder (1 in 100,000 to 250,000 births) where cells cannot correctly repair interstrand crosslinks (ICLs) resulting in genomic instability that can lead to bone marrow failure, and/or solid tumors. FA is associated with known mutations in at least 22 FA identified genes which occur more frequently among communities with consanguineous marriages as Egypt. We aimed to introduce immunodetection & Western-blotting to identify FA genetic subtypes and then target the pathogenic mutations on the molecular level among the studied patients. Patients and Methods: Five patients (4 females and one male) clinically diagnosed as FA were referred from the Hereditary Blood Disorders Clinic (HBD) for confirmation by chromosomal breakage analysis using Diepoxybutane (DEB). Using western blotting, FANCA protein was detected in skin fibroblasts derived from FA and controls. Molecular confirmation using Multiplex ligation-dependent probe amplification (MLPA) to screen deletion mutations in the FANCA gene followed by a targeted panel includes three FANC genes. Results: Immunodetection of FANCA protein in four patients showed different patterns of FANCG and FA associated peptide 24 (FAAP24). Two patients with the same mutation showed a similar profile of FA core complex detected by FANCA antibody. Two patients had a normal profile. Confirmation by MLPA detection of intragenic homozygous deletions of FANCA gene. NGS targeted panel characterized two FANCA and one FANCL variants.