Inherited gene mutations, insertions, deletions of single genes cause most of the rare diseases. Oligonucleotide therapeutics represent one of the most flexible platforms for developing drugs for rare diseases. Presently, 15 oligonucleotide therapeutics have been approved in the United States of America (USA) to treat various rare diseases and 4 oligonucleotide therapeutics (eteplirsen, golodirsen, viltolarsen and casimersen) are used to treat Duchenne muscular dystrophy. The progress of oligonucleotide therapeutics in Japan has emerged from several decades of basic research. In March 2020, viltolarsen, developed by Japanese companies, was approved as a treatment for Duchenne muscular dystrophy. This article discusses the research and development of oligonucleotide therapeutics for rare diseases from the viewpoint of the proprietary technologies in Japanese pharmaceutical and bio-venture companies.