A cikin hunturu na 1996, an kwantar da ita a asibiti da ciwon huhu. A shekara ta 1997, ta zama mai rauni sosai, tana magana da cin abinci kaɗan, kuma ana tsoron za ta mutu. Ta nuna alamun rashin hankali a cikin shekarunta na ƙarshe. A watan Mayu 2003, an gano wata mummunar cuta a wuyan Hepburn. An yanke shawarar kada a shiga tsakani ta hanyar likita, kuma ta mutu daga bugun zuciya a ranar 29 ga Yuni, 2003, wata daya bayan ranar haihuwarta ta 96 a gidan dangin Hepburn a Fenwick, Connecticut. An binne ta a Cedar Hill Cemetery a Hartford. Hepburn ya so cewa ba za a sami hasken wuta ba.
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