A storage container in which a gas permeable covering sheet with impermeable gas permeability is thermally adhered to the opening edge of a container body containing a medical instrument is housed in an autoclave and sterilized with high pressure steam to prevent peeling of the cover sheet Providing a method of sterilizing the instrument. A method for sterilizing a medical instrument includes storing a storage container (12) in which a gas permeable and non-microparticulate cover sheet is thermally bonded with a thermoplastic resin to an opening edge of a container body housing a medical device in an autoclave (10) A temperature raising step of introducing high-pressure steam into the autoclave (10) to bring the inside of the autoclave (10) to a predetermined temperature, a step of keeping the interior of the autoclave (10) at a predetermined temperature for a predetermined time to sterilize the medical instrument , And a cooling step of cooling the interior of the autoclave (10) maintained at a predetermined temperature. In the step, compressed gas is introduced into the autoclave (10) which is in a steam atmosphere by introduction of high-pressure steam and autoclave ) Is pressurized to be equal to or higher than the pressure in the storage container (12).医療器具を収納した容器本体の開口縁に気体透過性で微粒子非透過性のカバーシートを熱接着した収納容器を、オートクレーブ内に収納し高圧水蒸気で滅菌しても、カバーシートの剥離を防ぐ医療器具の滅菌方法を提供する。 医療器具の滅菌方法は、医療器具を収納した容器本体の開口縁に気体透過性で微粒子非透過性のカバーシートを熱可塑性樹脂で熱接着した収納容器(12)をオートクレーブ(10)内に収納し、オートクレーブ(10)内に高圧水蒸気を導入してオートクレーブ(10)内を所定温度とする昇温工程と、オートクレーブ(10)内を所定温度で所定時間保持して医療器具に滅菌を施す滅菌工程と、所定温度で維持したオートクレーブ(10)内を冷却する冷却工程とを含み、前記工程では、高圧水蒸気の導入による水蒸気雰囲気下にあるオートクレーブ(10)内に圧縮気体を導入しオートクレーブ(10)内の現在圧力を収納容器(12)内の圧力以上に加圧する。