Inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders characterized by bone marrow failure, congenital anomalies, and an increased risk of malignancies. Diagnosis is often difficult due to the wide variety of clinical expressions. The representative diseases are Diamond Blackfan anemia (DBA), Fanconi anemia (FA), congenital sideroblastic anemia (CSA), congenital dyserhthropoietic anemia, Shwachman Diamond syndrome, and dyskeratosis congenita. Next-generation sequencing technologies have facilitated the discovery of germline mutations that cause IBMFS. Recently, Japanese groups have identified novel causative genes for DBA, FA and congenital thrombocytopenia by applying whole exome-sequencing. In this review, we will highlight recent studies on DBA, FA and CSA in Japan, which have employed next-generation sequencing technologies to elucidate the genetic etiology of IBMFS.