The clock is ticking for airline passengers stranded on the tarmac. A Department of Transportation ruling that goes into effect Thursday prohibits airlines from keeping flights in limbo on the runway for more than three hours and guarantees affected travelers a few basic rights in the interim, including food after two hours and working bathrooms.

Fewer than 1% of domestic flights experience delays of more than three hours, but more than 200,000 travelers are affected by those delays each year, says George Hobica, the founder of AirfareWatchdog.com.

Last summer, 47 passengers were detained on a plane overnight in Rochester, Minn., after weather diverted their 2.5-hour ExpressJet/Continental flight from landing in nearby Minneapolis. The DOT fined the three airlines involved $175,000 (including a $75,000 fine for Mesaba Airlines, which was the only staffed airline at the terminal during the incident) and began taking a more aggressive stance on delays. That incident was the straw that broke the camel s back, Hobica says.

Now, breaking the three-hour limit results in airline penalties of up to $27,500 per passenger. Transportation Secretary Ray LaHood told reporters in a conference call last week that the rule would be strictly enforced. LaHood also recently denied five airlines requests for temporary waivers to the limit at high-traffic airports in New York, Philadelphia and Newark, N.J.

The airlines say they plan to comply with the new regulations. We also want to make sure consumers know there will be cancellations caused by the ruling, cancellations that would not exist if not for the new rule, says David Castelveter, a spokesman for the Air Transport Association, a trade group representing carriers. He adds that carriers are likely to err on the side of caution (canceling more flights rather than risking fines) until there is more clarity about how the DOT will investigate delays and assess penalties.

Anne Banas, the executive editor for SmarterTravel.com, a travel advice site, says the airlines are unlikely to cancel many more flights to dodge fees. All those cancellations would be a customer service nightmare, she says. Travelers are already entitled to refunds for cancelled flights. Airlines scaled-back flight schedules would also limit their ability to rebook passengers, losing them more fares.

Congress may reinforce the ruling this year by signing it into law as part of the Federal Aviation Administration funding bill. That would make passengers new rights harder to overturn, says Kate Hanni, the founder of FlyersRights.org. (Hanni and her family were stranded on the tarmac for nine hours in 2006.) Any changes would likely toughen the existing regulation, she says.

Here's a look at what travelers can expect from their carriers now, based on the text of the new regulation.

Airlines are prohibited from:

Permit an aircraft to remain on the tarmac at large and medium hub airports for more than three hours without deplaning passengers

Airlines must return the plane to the gate or otherwise allow passengers to deplane before the three-hour mark, or face a fine per-passenger. International flights arriving in or departing from the United States must specify their own time limits in advance.

The ruling makes an exception if safety or security is at stake, or air traffic control determines that airport operations would be disrupted by a return to the terminal. That s a potentially important loophole, Hobica says. Gate space is a premium at most terminals, so it could prove relatively easy for an airline to argue that it was impossible to safely and securely deplane a waiting flight.

Scheduling chronically delayed flights

For some carriers, late flights are a habit. There are some flights out there that are actually late 80%, 90%, 100% of the time, says Tom Parsons, the chief executive for BestFares.com. Now, if airlines see a flight is usually an hour late, they must revise its schedule to leave an hour later, he says. The Bureau of Transportation Statistics now tracks flights of the worst offenders.

Some airlines are better than others at getting passengers to their destination on time. Check their record before you book.

Retroactively applying material changes to their contracts of carriage that could have a negative impact on consumers who already have purchased tickets

Even as airlines move quickly to add new fees, passengers are now guaranteed that the services and fee structures in place when they bought their ticket will apply when they travel. Airlines tried grandfathering in many of the checked-bag fees, but this rule halts that, Parsons says. However, if terms have changed in your favor, the newest version of the policy applies.

Airlines must:

Provide adequate food and potable drinking water for passengers within two hours of the aircraft being delayed on the tarmac

Airlines are likely to provide a bottle of water and a granola bar or similar inexpensive fare -- just enough to sustain passengers during a third hour on the tarmac. They re going to have something more than peanuts because of peanut allergies, Hanni says.

Maintain operable lavatories

Bathrooms are a pressing issue for stranded flights because airlines can t simply dump the waste as they would 30,000 feet up, Parsons says. Keeping the facilities in working condition requires a ground mechanic following waste-removal procedures.

If necessary, provide medical attention

Medical concerns have been a key issue in pushing passenger rights reform, Hobica says. Now airlines must provide medical attention to passengers in need. Passengers still should call 911 if they re having a life-threatening emergency, he says.

Respond in a timely and substantive fashion to consumer complaints and provide information to consumers on where to file complaints

The DOT has said it will actively investigate every complaint regarding airline delays, and this provision helps consumers be heard, Hanni says.

Display on their web site flight delay information for each domestic flight they operate

Before the new rules, most airlines reported delays only to the DOT. Starting in July, they must post the information on their own sites. It s good customer policy to let people know about delays, Banas says.