Although Frontier Airlines has gotten a lot of publicity in the past month for simplifying its fare structure and lowering its cheapest fares by an average of 12%, it also changed some baggage-checking fees: It now charges passengers buying its cheapest air fares $50 to carry on a bag, if the right isn't purchased until they reach the boarding gate.

Frontier's policies essentially copy those of other discount carriers such as Spirit (SAVE) and Ireland-based Ryanair (RYAAY), an earlier practitioner of unbundling of fares – which means passengers can pay only for services they truly need and want.

'Cheapest' Isn't Always Least Expensive

Despite the discount rhetoric, Frontier does not necessarily offer the cheapest fares on all routes it flies, if fees charged are factored in. On routes where it competes with Southwest, for example, Southwest (LUV) doesn’t charge passengers to change their tickets, nor does it charge them to check their first two bags; similarly, on JetBlue (JBLU) the first bag checked is also free. Purchasers of Frontier’s cheapest fares must pay $75 to change their tickets and anywhere from $20 to $75 to check from one to three bags.

The bottom line here, said Henry Harteveldt, travel-industry analyst for Atmosphere Research, is that today more than ever, ”there are no blanket answers to the question of what airline is offering the cheapest fare.

“You have to look at the total cost of the journey,” Harteveldt says, not only the base air fare but also additional fees for booking a preferred seat location, extra legroom, priority airport screening, priority boarding and checking baggage. Unfortunately, there is no one tool out there to help you analyze this.

This could change if new consumer protection rules proposed by the Department of Transportation on May 21, 2014, with a 90-day comment period, go into effect. The proposed rules include mandating that airlines and ticket agents, including internet search sites, disclose fees for the first checked bag, second checked bag, one carry-on item and advance seat assignment. Currently, airlines are required to list these fees somewhere on their websites, but they don't have to warn customers about them before they book or specify which fee applies to the itinerary the customer is considering.

Meantime, you'll need to do a fair amount of detailed research to determine which fare is the best bet for you.

Comparing Fees, Not Just Fares

Online travel agencies such as Expedia, Orbitz and Priceline, and Web sites such as Kayak and Hipmunk, which compare fare information from multiple sources, can show you fares charged by many airlines, but they generally don't include information on fares from low-cost carriers such as Southwest and Allegiant (ALGT). Nor do any sites provide extensive details on all fees charged by each airline; to get this, you must check each airline’s Web site, where all fee information is outlined at length, as required by the U.S. Department of Transportation.

An exception, says George Hobica, president of Airfarewatchdog, a Web site owned by TripAdvisor that provides low-fare lists, alerts and advice, is the TripAdvisor Flights Web site, which not only compares fares offered by airlines on the same route, but also provides details of fees they charge for baggage-checking, extra legroom and other amenities.

To figure out how to get the most bang for your buck when buying an airline ticket, Harteveldt recommends checking the Web sites of each airline you are considering. Hobica suggests registering to use Kayak – registered users get more in-depth, broader-ranging information on fare availability than those who simply use the site for a one-time search.

Special Advice

Also bear in mind that the way to tackle a fare search – and what constitutes the best deal – can differ according to the traveler’s goals and needs.

For parents. A mother traveling with two children and three suitcases on a family vacation to Walt Disney World in Orlando should definitely research the baggage-checking fees charged by carriers she’s considering; She should also remember that Delta (DAL), for one, offers free snacks in Economy on flights under 900 miles. She also might more easily find three seats together for her family on a Delta flight than on a deeply-discounted carrier.

For last-minute getaways. Hobica recommends using Priceline, whose name-your-own pricing policy lets you submit the fare you are willing to buy, but doesn’t let you stipulate which carriers you would fly. The site “has the best last-minute fares, which you bid for. I recommend Priceline if your trip is really last-minute,” he said.

If you can be flexible. Other ways to possibly get cheaper rates, says Hobica, are to be flexible about the dates you are willing to travel and the airports you are willing to use. “There are always alternate airports that are cheaper,” he says, noting that fares into and out of Silicon Valley’s Norman Y. Mineta San José International Airport recently have been $100 cheaper roundtrip than fares to and from airports in nearby Oakland and San Francisco.

One downside of flying out of a secondary airport, says Harteveldt, is that fewer flights might be available there than at a larger, neighboring airport that could possibly provide “a more convenient journey.”

Not surprisingly, Hobica also recommends registering with Web sites such as Airfarewatchdog that will send you price alerts; others include SmarterTravel (also owned by TripAdvisor), Kayak, FareCompare , Yapta and TripAdvisor Flights. Also sign up for alerts from the airlines you patronize.

The Bottom Line

“A vacation is a significant investment. You have to take the time to do your homework to get the best value. You have to look beyond just the price – the cheapest fare may come with a terrible price to be paid,” warns Harteveldt.

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