A few months ago, the nation’s three major airlines quietly tweaked their fare rules. The result? Travelers encountered notably higher prices for certain multicity round-trips and open-jaw trips.

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A few months ago, the nation’s three major airlines quietly tweaked their fare rules. The result? Travelers encountered notably higher prices for certain multicity round-trips (visiting several cities by plane) and open-jaw trips (flying into one city, traveling to another by, say, car or train, then flying home from that city).

Take, for instance, Kevin Mitchell, chairman of Business Travel Coalition, an advocacy organization that ran a search for a domestic trip and found a whopping $1,200 coach fare. The trip was from Jacksonville, Florida, to Los Angeles and then (after taking a rental car to San Francisco) from San Francisco to Jacksonville, a popular vacation route, Mitchell said in a news release. If priced as two one-way tickets instead, the fare was one-third as much: $400. “Most consumers,” he said, “especially the majority who are infrequent travelers, will not be aware and will pay dearly when booking online at an airline website.”

So what exactly is going on? How widespread is this pricing discrepancy? And are there ways to avoid getting fleeced?

Gary Leff, an airline industry expert and the author of the blog View From the Wing, said the issue, in a nutshell, is that to compete with ultra low-cost carriers, like Spirit Airlines and Frontier Airlines, the major airlines are selling cheaper tickets in certain markets. What they don’t want, however, is for travelers to get creative and piece together a couple of cheap fares from, say, San Diego to Dallas plus Dallas to Orlando, Florida, because the airlines never intended to offer rock-bottom fares from San Diego to Orlando. The fare rule changes rolled out in the spring were meant to prevent that sort of frugal workaround from happening. But in the process, some multicity and open-jaw fares went through the roof. “They don’t have the perfect strategy yet and they’re trying to learn,” Leff said of the airlines. “It’s new territory for them.”

To see just how likely one is to come across these more costly fares, I’ve been running various searches on the websites of American Airlines, Delta Air Lines and United Airlines. On the bright side, I didn’t encounter many instances of these exorbitant fares. For example, when pricing a June ticket on United.com from New York to Chicago, and then from Detroit to New York, the fare was $334.20. If I were to book that trip using separate flights, traveling at the same times, it would be $51 more: $385.20. The open-jaw ticket was indeed cheaper than purchasing separate one-way tickets.

Additionally, much to my surprise, when running a multicity search among New York; Fort Lauderdale, Florida; and Chicago on United’s website, a note appeared: “Using multiple one-way searches may return lower fares,” it said. A helpful (and most unexpected) tip.

But not all searches go quite so well. On the American Airlines website I ran a search starting in San Francisco and flying to Portland, Oregon, then flying from Seattle back to San Francisco. American priced that trip as $2,081.20 nonstop in economy. Priced instead as two one-way flights for the same dates on AA.com (from San Francisco to Portland and then from Seattle to San Francisco), it was $334 nonstop in economy, nearly $1,750 cheaper.

The Business Travel Coalition has estimated that the airlines’ nascent rules could drive some fares up by as much as seven times. That’s the bad news. The better news is that Leff, who wrote about the tightening of American’s fare rules on his blog on BoardingArea.com in March, said that such glaring price discrepancies are not as prevalent as they were even two months ago.

“What we’re seeing is testing in limited numbers of markets,” he said, adding that it took the airlines a little while to catch on to the fact that the changes they made to solve one problem unintentionally created another: eye-popping multicity fares. “It was taking a jackhammer to swat an ant.”

All of this means that when flight shopping on an airline’s website you must take time to price your trip in different ways, as well as make use of the various search options.

Make sure to set your search preferences for the lowest available or best fare, not a refundable fare (which will be higher). All three major U.S. airlines allow you to adjust that. To be sure you’re getting the best price on a multicity trip, run a search for the trip as a round-trip ticket as well as separate one-way fares. In some cases you may want to consider a round-trip ticket between the cities where you plan to start and end your trip, along with a couple of one-way tickets in between.

If sticking to your budget is the priority, you may find that it makes more sense to fly with an ultra low-cost carrier, even for part of your trip.

Just keep in mind that there’s no hard and fast rule when it comes to fares. Sometimes it will pay to book each leg as a separate one-way ticket; other times a round-trip will be cheaper. A recent search on Delta.com for a multicity trip in June with flights in the main cabin from New York City to Miami and then from Orlando back to New York City wasn’t just cheaper than booking each leg separately: It was nearly half the cost, approximately $320, in contrast to about $630.

Leff thinks the high prices that are turning up for certain trips as a result of the fare rule tweaks will ultimately go away, though it may take some time.

“In the meantime people need to spend extra attention,” he said. “There’s more work for the consumer to make sure they’re getting the best deal.