Andhra Pradesh Governor E S L Narasimhan, Chief Minister N Kiran Kumar Reddy and other leaders saw him off at the Begumpet airport.
Mukherjee had arrived here on December 26 and inaugurated the World Telugu Conference held in the temple town of Tirupati and took part in events organised in Tamil Nadu and also Maharashtra.
During the sojourn, the President stayed at the Rashtrapati Nilayam at Bolaram here.
Rashtrapati Nilayam is one of the two official retreats of the President of India, the other being 'The Retreat Building' in Shimla.
According to Rashtrapati Bhavan website, the buildings -- one in North and another in South--are "indicative of the integrative role of the Office of the President of India in our country".
It is customary for the President of India to visit the Rashtrapati Nilayam here and stay there at least once a year and conduct official business from the Nilayam.
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The Nilayam was taken over from Nizam of Hyderabad after the country attained independence.
Located at Bolarum in Secunderabad, this 11-room single storey building, spread in over 90 acres, has been handed over to the President's Secretariat as per the convention.