Sorenstam, the LPGA's top money-winner, has been bothered by a cold since last week's U.S. Open. She teed off at 12:30 PM, and was 1-over par through six holes.
She walked off the course after hitting her second shot on the par-4 7th into a greenside bunker.
'I'm feeling bad for the fans and the tournament, but my whole body feels ill,' Sorenstam said in a statement before leaving Point Grey Golf and Country Club.
Sorenstam said she was worn out from both the U.S. Open and the attention she has received since playing in the Colonial on the PGA Tour in May.
'I was hoping the last couple of days with rest would have made me feel better but the last couple of months have caught up with me,' she said. 'I tried my best to play today and I apologize to the fans but I need to go home and get better.'
Sorenstam said before this week's $1.3 million tournament started that she was still feeling the effects of a cold that bothered her at the U.S. Open.
Sorenstam shot a 2-over 73 Sunday and missed Monday's 18-hole playoff, which Hilary Lunke won over Angela Stanford and Kelly Robbins.
Sorenstam won the 2001 Canadian Open in Ontario, but missed last year's tournament to play an event in her native Sweden.
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