Vajpayee, a bachelor, is survived by his adopted daughter Namita Kaul Bhattacharya. He is cremated on Friday in New Delhi.
"It was the exemplary leadership of Atalji that laid the foundations for the prosperous and inclusive India in the 21st century," said Prime Minister Narendra Modi, who led the nation in the mourning of the stalwart whose popularity went right through the party lines.
Vajpayee's death was announced by the All India Institute of Medical Sciences (AIIMS) hospital, where he was admitted on June 11 with a variety of ailments.
"It is with great sadness that we inform about the sad demise of the former Prime Minister of India, Shri Atal Bihari Vajpayee, at 5:05 am", said the AIIMS in a statement.
It said that his condition had been stable for the past nine weeks, but "unfortunately his situation deteriorated in the last 36 hours and he was put on life support systems."
When it became clear that the end was near, many politicians and benefactors had gathered at AIIMS since the morning. A hint of gloom descended on the BJP headquarters as soon as news broke over Vajpayee's downfall.
Modi said Vajpayee's death is a "personal and irreplaceable" loss to him and that his futuristic policies in various sectors touched the lives of every citizen of India.
"It was because of the perseverance and struggle of Atal Ji that the BJP was built brick by brick," Modi said in a tweet.
"He traveled throughout the width and breadth of India to spread the message of the BJP, leading to the BJP becoming a strong force in our national government and in different states," he added.
A seven-day mourning in the state was announced by the government as a sign of respect for Vajpayee.
Vajpayee, who joined the Rastriya Swamsevak Sangha (RSS) in 1947, rose through the ranks and became one of the champions of the BJP and was the first non-Congress prime minister to complete a term of office.
In the evening, Vajpayee's body was taken to his home in Krishna Menon Marg, New Delhi, where many leaders cut parties and gave people from different layers of the population their last honors.
Seen as a moderate face of BJP, Vajpayee became prime prime minister in 1996, leading to a shaky coalition whose members were suspicious of BJP's right-wing politics. It took 13 days and collapsed after the loss of a vote of no confidence.
His second period as prime minister was in 1998 when the National Democratic Alliance came to power again, but that lasted only 13 months.
Finally, the NDA with Vajpayee as PM returned to power in 1999 and was voted out in 2004.
A lifelong bachelor, Vajpayee was first elected to Lok Sabha in 1957 of Balrampur in Uttar Pradesh in the second general election of India. His first speech in Parliament impressed his colleagues and colleagues that the then Prime Minister Jawaharlal Nehru Vajpayee introduced to a visiting foreign official: "This young man will one day be the Prime Minister of the country. . "
He remained a member of parliament for 47 years – ten times chosen for the Lok Sabha and twice for Rajya Sabha.
Vajpayee's signature in politics was to reach a pragmatic consensus, and in this process he earned the respect of his party, allies and opponents. In other countries, he projected a harmonious image of India and linked it to the world through his foreign policy
The former prime minister was admitted to the hospital on 11 June with an infection of the kidney canal, urinary tract infection, low urine production and congestion on the chest.
Vajpayee was a diabetic and had only one functional kidney. He suffered from a stroke in 2009 that weakened his cognitive skills. Then he developed dementia.
Vajpayee was born on December 25, 1924 in Gwalior, Madhya Pradesh, in a teacher, Krishna Bihari Vajpayee and Krishna Devi. Today, his birthday is celebrated as "Good Governance Day."
After graduating, he graduated from Victoria College in Gwalior, now known as Laxmi Bai College. He did his MA in politics from DAV College in Kanpur. After a brief flirt with Communism, in 1947 he became a full-time employee of RSS.
In his tribute, BJP president Amit Shah said he was a "rare politician, brilliant speaker, poet and patriot, his downfall is not only an irreparable loss to the BJP but also to the entire country."
Congress chairman Rahul Gandhi said on Twitter: "Today, India lost a great son. President of the Prime Minister, Atal Bihari Vajpayee ji, was loved and respected by millions. He gave my condolences to his family and all his admirers. We will miss him . "
Manmohan Singh, who succeeded Vajpayee as prime minister in 2004, welcomed the BJP as a great patriot and as one of the modern leaders of modern India & # 39; s who were in the service of the country all his life.
Amit Shah said that the last rites Vajpayee will take place Friday at 4 pm in Rashtriya Smriti Sthal. The body would be brought to the BJP headquarters at Deen Dayal Upadhyay Marg around 9:00 am and the funeral procession at 1:00 pm would leave the party office.