Fanconi anemia (FA) is an inherited bone marrow failure syndrome characterized 
by multiple congenital abnormalities, progressive bone marrow failure, and a 
predisposition to malignancies, resulting from mutations in one of the 22 known 
FANC genes (from FANCA to FANCW). The proteins encoded by these genes 
participate in a deoxyribonucleic acid interstrand cross-link repair pathway, 
the so-called FA/BRCA pathway. The 22 FANC genes include hereditary breast and 
ovarian cancer susceptibility genes, such as BRCA1 or BRCA2. Patients with FA 
display a wide range of clinical phenotypes owing to the genetic heterogeneity 
of the disease; therefore, the molecular diagnosis is critical for the 
appropriate management of such patients. Recently, we successfully subtyped 97% 
of the 117 Japanese patients with FA and identified 215 mutant alleles through a 
comprehensive strategy. In this review, the characteristics of genetic subtyping 
and mutated FANC gene variants in Japanese patients with FA and the 
genotype-phenotype correlation in FA are summarized. In addition, the carrier 
frequency of pathogenic FANC genes and risk of cancer among the FANC gene 
mutation carriers in general Japanese population are discussed.