EPA spokesman John Millett said fine particle pollution is a new standard for the agency.
The EPA released the list on Dec. 17, but Washington and Berkeley county officials said last week that they already knew they would be on it.
Neither county meets federal ground-level ozone standards.
The last few years, both counties have worked on comprehensive plans for air quality improvements.
Ground-level ozone, commonly thought of as smog, is created when the sun bakes pollution from vehicles, industry, consumer products and power plants, according to a Pennsylvania Department of Environmental Protection primer.
Fine particle pollution comes from both natural sources, such as smoke, and man-made sources, such as power plants and factories, the EPA said.
Fine particle pollution - about one-thirtieth the size of a human hair - "can aggravate heart and lung diseases and has been associated with a variety of serious health problems, including heart attacks, chronic bronchitis and asthma attacks," according to the EPA.
Berkeley County Administrator Deborah Hammond said Thursday that the county's Clean Air Task Force has created a plan that covers both ground-level ozone and fine particle pollution.
The plan was approved by the West Virginia Department of Environmental Protection and is awaiting approval by the EPA, Hammond said.
Jefferson County, W.Va. - which is not on the fine particle nonattainment list, but does not meet ground-level ozone standards - is part of the Clean Air Task Force, along with the City of Martinsburg, Hammond said.
Washington County Administrator Rodney Shoop said the county has worked closely with the Maryland Department of the Environment on its plan.
"There's more work to be done," he said.
Twenty states and Washington, D.C., are on the newly released fine particle pollution list.
All or part of 224 counties nationwide are on the list, while 2,909 counties are not on the list, which means they meet the standards.
Millett said some counties are on the list only because they are in metropolitan areas with air quality problems, not because those counties themselves have problems.
Locally, Frederick County, Md., also is on the list. Jefferson and Morgan counties in West Virginia and Franklin and Fulton counties in Pennsylvania are not.
The American Lung Association's 2004 "State of the Air" report, released in April, gives Washington, Frederick and Franklin counties a letter grade of "F" for their ground-level ozone levels.
Fulton, Jefferson and Morgan counties were not examined. Berkeley County's three-year data was considered incomplete and was not considered.
For particle pollution, the 2004 report says Washington County passes and Berkeley County fails.
Other Tri-State counties were not graded.
The American Lung Association says this is the first time its annual "State of the Air" report has considered particle pollution, such as power plant emissions, diesel exhaust and burning wood.