The 24-year-old Lee, who is searching for a first professional victory, took full advantage of his straight driving game to hit nine birdies against a bogey and a double bogey at Haesley Nine Bridges Golf Club in Yeoju.
Choi, an eight-time winner on the PGA Tour, opened with a 67 for tied second place in the $750,000 event sanctioned by the Asian Tour and Korean Golf Tour.
Another young Korean, Kim Do-Hoon, a former Asian Games team gold medal winner, also returned a 67, while American star Anthony Kim stormed home in 31 for a 68.
He was two strokes off the pace with Australians Scott Hend and Adam Groom.
Lee did not miss a single fairway as he attacked the pins relentlessly. Despite blemishes on two holes, a birdie conversion from 24 feet on 17 gave him the overnight lead.
"That was my best putt. Before the round, I knew the course was difficult but I had a good feeling with my game today," said Lee, whose card included four straight birdies on the front nine.
"It's good I'm in a high position and also above K.J. I have a lot of respect for him as he helped me once when I was a junior.
"He came to my hometown seven years ago and gave a clinic and I was amongst those who had the opportunity to learn from him. I will always remember that experience."
The 41-year-old Choi, an Asian Tour honorary member, fired an early warning that he was ready to win his own event after sinking seven birdies against two bogeys.
It was an eventful day for Choi, the world's number 14, as his round included a forgettable four-putt bogey at the seventh.
"I started a bit slow as I woke up at 5:00 am and it was very cold outside. The body was a bit slow but the sun came out very quick which made it warm," said Choi.
"I made mistakes on seven and nine but five under is a good position. I'm in a rhythm right now and I think my four rounds will be pretty steady."
Anthony Kim, who has three wins in the US, turned on the style with his putter as he came home with five birdies after turning in 37.
"I haven't hit the ball that well in a long time," enthused the former Ryder Cup star who was out of action earlier in the season due to thumb surgery.
K.J. Choi upstaged at own event
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