In the last 150 years, prospectors and energy companies have drilled as many as 12 million holes across the U.S. in search of oil and gas. Many were plugged after they dried up. But hundreds of thousands were simply abandoned and forgotten, often leaving no records of their existence.

Government reports have warned for decades that abandoned wells can provide pathways for oil, gas or brine-laden water to contaminate groundwater supplies or to travel up to the surface.

New wells sometimes disturb layers of rock and dirt near fragile old wells, leading to new cases of contamination. For Pennsylvania and other states sitting on top of the Marcellus Shale formation, the rapid growth of gas drilling may increase the danger of such contamination.

Abandoned wells have polluted the drinking water source for Fort Knox, Ky., and leaked oil into water wells in Ohio and Michigan. Similar problems have occurred in Texas, New York, Colorado and other states where drilling has occurred.

In 2008, gas from an abandoned well leaked into a septic system in Pennsylvania and exploded when someone tried to light a candle in a bathroom, killing the person, according to a 2009 draft report by the state Department of Environmental Protection. That report also documented at least two dozen other cases of gas seeping from old wells, including three where the drilling of new wells “communicated” with old wells, leaking gas into water supplies and forcing the evacuation of a home.

In February, methane from an old well made its way into the basement of a house in West Mifflin, triggering a small explosion. Two families were evacuated and have not yet returned.

Such incidents rarely receive much attention outside the states and neighborhoods they affect. But as the nation’s latest drilling boom continues, abandoned wells have begun attracting more attention, particularly in states where the earth is already pock-marked with holes left by earlier waves of extraction.

The most recent effort to count the nation’s unplugged wells was a survey published in 2008 by the Interstate Oil and Gas Compact Commission, a multistate agency made up of regulators and industry representatives. It found that states had located nearly 60,000 wells that needed to be plugged, and estimated that as many as a million more may be out there.

In Pennsylvania alone, regulators estimate that 184,000 wells were drilled before records were kept. Many were plugged with stumps, rocks or nothing at all.

The task of finding, plugging and monitoring old wells is daunting to cash-strapped state governments. A shallow well in good condition can sometimes be plugged with cement for a few thousand dollars. But costs typically run into the tens of thousands, and a price tag of $100,000 or more isn’t unusual.

More than two decades ago, federal scientists determined that chlorides, or salts, were leaking through abandoned wells and into an aquifer that supplies drinking water to nearly 40,000 people in Fort Knox. Mike Unthank, a scientist with the U.S. Geological Survey, said the problem could be solved if a few dozen abandoned wells were plugged.

But the bids that Kentucky’s Division of Oil and Gas received were so high that the Fort Knox project alone would deplete its $1.3 million plugging fund.

Some regulators fear that the number of abandoned wells will grow when the current drilling boom runs its course. To prevent that, states require energy companies to post bonds before they begin building their wells. But they are often so low that it can be more economical for a company to forfeit its bond rather than plug its wells. In Pennsylvania, for instance, an energy company can cover hundreds of wells with a single $25,000 bond.

John Hanger, who until January headed Pennsylvania’s Department of Environmental Protection, called the bonds “scandalously low.”

“There are some choices you shouldn’t put in front of even good companies,” he said. “I’d like to think the companies would do the right thing, but we know that just isn’t always the case.”

One of Pennsylvania’s worst cases of gas migration occurred in Versailles. From 1919 through 1921, more than 175 gas wells were drilled in the town. Residents put wells in their back yards to heat their homes, packing them into the 25-by-100-foot lots.

The boom dried up when most of the wells proved unproductive. But in the 1960s, pockets of gas began leaking into homes. Some houses were condemned and demolished, and Versailles eventually became a case study for federal scientists trying to locate old wells.

Some of the old wells were plugged. But more often, vents were installed to direct gas away from the homes. Today, dozens of pipes pop out of the ground in yards, behind garages and through houses, slowly leaking methane and hydrogen sulfide so the explosive gases don’t accumulate. In 2009, Versailles received a $368,600 federal grant to maintain its aging vents. About 50 methane alarms have been installed in the town.

The vents and alarms are just part of life in Versailles. Mayor James Fleckenstein recently bought a house with two vents on the property and an alarm in the kitchen.

“We’ve been living with this problem forever,” Mr. Fleckenstein said. “People would have a vent in their yard burning 24 hours a day all year long, a one-inch pipe sticking out of the ground. People would put a coffee can and light it and it would just burn all the time.”

There’s no longer enough pressure in the gas formation to make the vents flammable, Mr. Fleckenstein said, and the town hasn’t had any problems with migrating gas for a couple of years. But that could change at any time, said Fred Baldassare, who for years oversaw gas migration cases for the Department of Environmental Protection and now runs a consulting business.

In February, gas from an abandoned well caused a small explosion across the river in West Mifflin. The gas company evacuated the house where the explosion occurred, and the house next door, where Nick Kellington lived with his wife and four children.

“I said ‘How long are we packing for?’ and he said ‘I don’t know,’ ” Mr. Kellington said. “Somebody tells you that, what do you do?”

Mr. Kellington said the DEP, which declined to comment about the case, used old maps to identify a nearby well that may be the source of the gas. The Kellingtons are renting a townhouse while they wait for a state-hired contractor to fix the problem.

Every time the Kellingtons visit their former home, a gas company employee must first test the temporary vent that sticks out of their basement window. Even then, Kellington has to leave his cell phone outside, lest a spark ignite a pocket of gas.

Finding and plugging an old well can be risky, because nearby wells may be disturbed and begin releasing gas. So the Kellingtons’ home is being fitted with a system that pumps air under the house, creating a high-pressure zone that would prevent gas from leaking indoors.

Mr. Kellington said that even if the system is installed successfully, he may try to sell the house and move.

“My wife just doesn’t feel safe,” he said.

Edwin Drake drilled the nation’s first commercial oil well near Titusville, Pa., in 1859, and for decades people across the country drilled wells as they pleased. Some states didn’t develop modern regulations until the second half of the 20th century.

In the early days, the industry was dominated by “wildcatters” looking to get rich. Those who didn’t get rich often ran out of money before they could plug or seal their wells.

Nobody knows how much damage abandoned wells have caused over the years. Most states don’t systematically track cases of contamination that result from abandoned wells, said Mike Nickolaus, special projects director for the Ground Water Protection Council, an association of state groundwater agencies.

Despite the lack of comprehensive data, state and federal reports have chronicled scores of contamination cases over the last couple of decades.

The EPA’s 2004 study of hydraulic fracturing examined groundwater contamination in the San Juan Basin in Colorado. The report said state authorities suspected that gas migration into water wells and buildings was due, at least in part, to the presence of abandoned wells.

Some regulators are concerned that fracking, which is used in most new wells, increases the possibility that old wells will be damaged or disturbed. The process injects water, sand and chemicals into wells at high pressure to release oil or gas. But by disrupting the earth it can also push gas and other contaminants into openings created by old wells.

That’s what investigators think happened on a rainy day in 2006, when gas and water began spewing out of the ground on Emile Alexander’s farm in Washington County. Investigators determined that the fracking of a new well caused methane to leak through an abandoned well and into the ground and the aquifer. Some water wells near Mr. Alexander’s farm have been fitted with vents to allow stray gas to escape. Methane gas isn’t toxic to ingest, but it can explode.

Although Mr. Alexander receives royalty payments from two wells on his land, he wishes he had never signed the lease. “I didn’t sign it to kill me,” he said.

In an internal briefing last year, EPA scientists raised concern that fracking near Pennsylvania’s many abandoned wells could threaten groundwater, saying the old wells “may present a risk unique to the hydrofrac process.”

This year, as part of its first comprehensive study of hydraulic fracturing, the EPA plans to look at whether abandoned wells might become conduits for fracking fluids.

Mr. Hanger said the way states handle today’s drilling rush will determine how this boom eventually plays out.

“I personally think one of the very good things that’s coming out of the Marcellus is a whole lot more attention to the problems that were created in the past and the opportunity to do it better this time,” he said. “If we don’t raise the bonding amounts, we’re repeating a mistake.”