Koizumi flew out of Tokyo's Haneda airport on board a government Boeing 747 at 06:48 am (2148 GMT Friday). The flight to Pyongyang was scheduled to take approximately two-and-three-quarter hours.
Koizumi will meet with Kim Jong-Il during the one-day trip for his second round of talks with the reclusive leader following their historic summit in September 2002.
The first summit resulted in the return of five Japanese citizens kidnapped in the 1970s.
Hopes are high in Japan that Koizumi will bring back their eight relatives, including a former US soldier, listed as a deserter, who is married to a Japanese abductee brought back to Japan with two other couples in October 2002.
Immediately before boarding his flight, Koizumi told reporters the main aim of his trip was to "turn hostile relations between Japan and North Korea into amicable relations."
"I will do my utmost efforts so that the eight people will be able to come to Japan," he said.
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