By Kyle Peterson

CHICAGO (Reuters) - American Airlines cancelled more than 1,000 flights, or nearly 45 percent of its daily schedule, on Wednesday, stranding thousands of passengers and creating chaos at the busiest U.S. airports as it conducted safety inspections of its MD-80 aircraft.

The cancellations by the No. 1 U.S. airline, a unit of AMR Corp, follow 460 cancellations on Tuesday and hundreds of cancellations two weeks ago, also for inspections.

An airline spokesman said about 30 MD-80s were in service on Wednesday morning and more were expected to resume flying later in the day.

"We continue to inspect every airplane to ensure we are in total agreement with the specifications of the directive," AMR Chief Executive Gerard Arpey said in a statement. "We will get back to a full schedule as quickly as possible."

Shares of AMR fell more than 10 percent early Wednesday afternoon, outpacing losses by other U.S. airline stocks. The Amex airline index was down 4.8 percent.

American said in a statement on Tuesday that the Federal Aviation Administration (FAA) raised new concerns about recent wiring inspections of the narrowbody MD-80 aircraft that resulted in cancelled flights two weeks ago. MD-80s make up nearly half of AMR's fleet. The average age of the AMR MD-80s is 18 years.

The inspections are part of an industrywide FAA review of airline compliance with agency safety directives. Several carriers have grounded aircraft as a result of the audit, which was triggered by inspection and maintenance lapses at Southwest Airlines Co.

The American inspections relate to a 2006 FAA order to ensure that wiring in MD-80 wheel wells is properly installed and secured.