Kim visited the Kumsusan Palace of the Sun in Pyongyang where Kim Jong Il lies in state, the Korean Central News Agency reported.
Kim paid his respects before statues of his father and grandfather, the newspaper said, quoted by Yonhap News Agency.
Kim Jong Il's birthday is considered a holiday in the communist country, called the Day of the Shining Star, Yonhap reported.
More than 10,000 citizens and military personnel presented flowers and bowed deeply during a moment of silence before the statues, Japan's Kyodo News reported.
Kim's wife, Ri Sol-ju, was not in attendance at the ceremony, Yonhap reported.