Earlier, Kim had proposed the meeting be extended so that Roh could have lunch on Thursday with the North Korean leader.
But Roh did not immediately agree and it was unclear whether Roh rejected the offer or if Kim took it back.
Roh's spokesman said: "We estimate that the talks were sufficient and candid and have achieved good results. President Roh himself said he was satisfied with the outcome."
Roh had said he wanted the summit to mark the start of a genuine peace process. He has suggested he is ready to increase aid to the impoverished North Korean economy.
More than 50 years after a ceasefire halted the Korean War, North and South remain officially at war and there are hopes that this summit might finally pave the way to a formal peace treaty.
Wednesday's talks saw the two leaders apparently more at ease with each other after what many commentators saw as a chilly reception from Kim to his South Korean visitor.
At Tuesday's welcoming ceremony, the North Korean leader barely smiled and exchanged only a few words with his guest.
Later Kim also failed to show up at an evening banquet thrown by the North Koreans, instead sending his deputy, Kim Yong-nam, to play host.
The body language was in stark contrast to the enthusiastic reception given to Kim Dae-jung, the then South Korean president, during the first inter-Korean summit in 2000.
|A tale of two welcomes... Kim Jong-il on Tuesday, left; and, right, in 2000 [GALLO/GETTY]|
Seven years ago the North Korean leader spent over two hours with the South Korean on the day he arrived, compared with barely 12 minutes given to Roh.
But at their meeting on Wednesday the frost appeared to have thawed somewhat, with Kim repeatedly smiling and noticeably more animated as he welcomed Roh to their first formal round of talks.
The meeting began with an exchange of gifts, with Roh giving his host a bookcase containing DVDs of South Korean soap operas and films starring Lee Young-ae, believed to be Kim's favourite actress.
The North Korean leader is known to be a film fan and is said to have a vast personal movie library.
According to South Korean pool reports, the talks at the Paekhwawon state guest house in Pyongyang included Roh speaking of his concern about the summer floods in North Korea that left some 600 dead or missing.
The floods, which also left tens of thousands homeless, had caused the summit to be pushed back from its originally scheduled date in late August.
|Kim did not show up for a banquet in Roh's |
honour on Tuesday evening [AFP]
Further talks are expected to take place on Wednesday afternoon, although no specific agenda has been made known.
Later the South Korean president is scheduled to attend an evening performance of the North Korean propaganda spectacle known as the "mass games".
It was not known if Kim would also attend.
Roh, who is in the final five months of an unpopular presidency, is under heavy pressure to bring with him concrete results when he heads back to Seoul on Thursday.
Critics in the South have said the summit is aimed at boosting domestic political support and unlikely to achieve much.
Roh has given few specifics about what he will propose or seek from the North Koreans during the summit.
Before travelling to Pyongyang, a senior aide to Roh described the summit objectives as "peace, prosperity and reconciliation, and otherwise open-ended".
Many want Roh to raise the issue of the North's nuclear weapons programme and human rights during the summit.
But sceptics say he is unlikely to touch on sensitive subjects for fear of offending his host.