The Department of Health and Human Services will start asking questions about sexual orientation and gender identity in its flagship survey of the health of the American population.

Starting in 2013, the National Health Interview Survey (NHIS) will include questions about sexual orientation along with those covering health insurance, usual site of medical care, vaccination, obesity, smoking, alcohol consumption and many other topics. Sometime later, questions about gender identity — a more complicated subject — will be added.

“We are taking critical steps toward ensuring the collection of useful national data on minority groups, including for the first time, LGBT [lesbian, gay, bisexual and transgender] populations,” Kathleen Sebelius, the Health and Human Services secretary, said in a statement.

The NHIS annually surveys about 40,000 households, collecting information on about 100,000 people. Its results are a representative sample of the entire country and are essential for both public health policymaking and academic study.

Questions about sexual orientation and behavior are already part of two surveys, the National Health and Nutrition Examination Survey, which both interviews and physically examines people, and the National Survey of Family Growth, which targets people of reproductive age. Neither of those surveys, however, is large enough to provide data on issues such as gender identity that can be generalized to the country as a whole, said Sherry Glied, assistant Health and Human Services secretary for planning and evaluation.

“The NHIS is the major one that we use to look at disparities in populations,” she said.

The decision was greeted enthusiastically by researchers and LGBT advocates.

“I think this is an in­cred­ibly important decision. We’ve been waiting for it for many years,” said Ilan Meyer, a professor of sociomedical sciences at Columbia University’s Mailman School of Public Health.

Researchers knew in the 1990s that gay, lesbian and transgender people constituted a population whose medical needs and experience with the health-care system were different from those of other groups. But the disparities couldn’t be understood in detail because most survey data couldn’t be analyzed on the basis of sexual orientation or identity, the way it could be with race or ethnicity.

“We’re invisible until they add us to these surveys,” said Scout, a transgender researcher at the Network for LGBT Health Equity in Boston who uses only one name.

“We suffer profound health disparities by many measures,” he said. “Discrimination is rampant. Counting us is the first step in fixing it.”

Before adding questions about gender identity, Health and Human Services will convene several expert panels to discuss what sort of questions should be asked and how much detail should be elicited. A person’s psychic identity and biological identity are not always the same.

Questions about sexual orientation will be field-tested in an expanded survey population for the 2012 NHIS. Experience in other surveys shows that some people don’t understand such questions, especially when they are translated into languages other than English. The goal will be to maximize the number of usable responses, Glied said.

One issue that will be addressed is whether to use an audio-equipped computer for asking and answering sex-related questions, so that the interview subject doesn’t have to answer the surveyor directly. The National Survey of Family Growth used such technology in its recent round when it asked about same-sex activities and infidelity.

The federal government has more than a dozen health surveys that seek information about topics as diverse as vaccination, diabetes, asthma, exercise, contraception, divorce and hospice care. While only some include sexual orientation and gender identity, such questions should be consistent among surveys so the results can be compared, Glied said.

In a related matter, Health and Human Services said that from now on, it will use a larger number of ethnic categories in its surveys to get a more detailed understanding of Hispanic, Asian and Pacific Islander populations. That is in response to the Office of Management and Budget’s new standards for all federal surveys.