Kalam, who would have turned 84 in October, was confirmed dead more than two hours after he was wheeled into the ICU of Bethany hospital in a critical condition following the collapse at around 6.30 PM.
Considered the most popular President, Kalam became the 11th head of the state and occupied the post between 2002 and 2007 but lack of consensus denied a second term in office for a man who came from outside political spectrum.
Chief Secretary P B O Warjiri told reporters outside the hospital that he had spoken to Union Home Secretary L C Goyal asking for necessary arrangements to be made for carrying Kalam's body from Guwahati to Delhi tomorrow morning.
"The former President has been admitted to Bethany hospital in a critical condition," M Kharkrang, SP Khasi Hills said earlier.
Doctors from the army hospital and North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS) rushed to Bethany hospital but their efforts proved to be of no avail.
Avul Pakir Jainulabdeen Abdul Kalam rose from humble origins to become the President in the most unexpected manner during the NDA government under Atal Bihari Vajpayee after an all party consensus minus the left parties that saw him through in an election which he won handsomely.
An aeronautics engineer from Madras Institute of Technology, Kalam was considered the brain of missile programme in India got and as Chief Scientific Adviser to Vajpayee was also instrumental in the Pokhran nuclear test in 1998.
A bachelor, the former President was a veena player and was deeply interested in Carnatic music. He was vegetarian all his life.
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