Mercedes-Benz, which ranked 25th in the survey just two years ago, ranked fourth overall this year, followed by Toyota's mainstream Toyota brand.
Ford's style-oriented Mercury brand was the top-ranked U.S. brand, coming in sixth overall.
Four General Motors brands - Cadillac, Chevrolet, Pontiac and Buick - scored above average, a feat not managed by any GM brands last year.
"I think the culture in the company has completely changed," said Jamie Hrescko, GM's vice-president for quality. Those four brands account for 82 percent of GM's sales volume, he said.
All three of Chrysler's brands - Chrysler, Dodge and Jeep - scored well below average. Jeep had the worst score of any overall brand.
The results do not reflect recent changes the company has implimented in its vehicles, Chrysler spokesman Ed Saenz wrote in an e-mail.
"The leadership at Chrysler is confident they will see significant improvement in both perceived quality and the customer dissatisfaction associated with the 'design' portion of IQS in the next survey," he wrote.
NEXT: Category: Sub-compact