Private companies are starting to grapple with the Supreme Court’s decision to strike down a key part of the Defense of Marriage Act, and some are finding that the changes they may have to make are more complicated than expected.

That’s particularly true in areas such as Washington, where a company’s employees often live in neighboring jurisdictions that have conflicting laws on gay marriage. Maryland and the District legally recognize same-sex marriage, while Virginia does not.

The conflicting statutes raise the question, for example, of whether a Virginia company with employees working in Virginia — but who live in, or got married in the District or Maryland — will have to extend family leave, pension and other benefits to those employees with same-sex spouses. There could also be tax consequences and beneficiary issues as well.

“There are still many questions about how that’s going to play out,” said Vicki Nielsen, an employee benefits attorney at Ogletree Deakins.

Much of the confusion stems from the Supreme Court’s decision to deem unconstitutional the denial of federal benefits to same-sex couples, while allowing states to decide for themselves whether to recognize same-sex marriage.

Because employment benefits are regulated by both state and federal laws, it is unclear what changes, if any, must be made by companies in the 37 states that do not recognize gay marriage. In those states, employees with same-sex spouses may be entitled to more rights under the federal Family and Medical Leave Act, which allows workers to take job-protected leave for family reasons, including caring for a spouse.

“If a same-sex spouse is ill and the employee needs to take leave, they may have FMLA rights they may not have previously had,” said Jason Rothman, a lawyer at Ogletree Deakins who advises companies on employee benefit plans.

The key word, however, is “may.” While FMLA is a federal mandate, it defers to state law for the definition of marriage — leaving companies in states that don’t recognize gay marriage scratching their heads over which authority’s law their policies should reflect.

“Now that the federal government recognizes gay marriage, the question becomes: Are same-sex partners now eligible for leave entitlements under federal law, even in states that don’t recognize gay marriage?” said Bruce Elliott, manager of compensation and benefits at the Society of Human Resources and Management Association. “Which entity will take primacy here? It’s not at all clear.”

The Family and Medical Leave Act is just one of the 1,000-plus federal laws and regulations affecting employee benefit plans that employers are waiting for federal agencies to clarify after the DOMA decision, Elliott said. Others include the Employee Retirement Income Security Act, or ERISA, which regulates pensions, and the Americans with Disabilities Act, which prohibits employers from denying an employee health coverage available to others because of a spouse’s disability.

Companies across the nation are beginning to grapple with those issues. Employers that already provide the same benefits for workers’ domestic partners as they do for workers’ spouses will not have to change much. About 62 percent of Fortune 500 companies already offer domestic partner health benefits, according to the Human Rights Coalition. But employers in the 12 states plus the District that recognize same-sex marriage — and do not already offer equal benefits — may have to revisit the way they define “spouse” in health and retirement plans.

The DOMA decision also does not address what happens when someone marries a partner in a state that recognizes same-sex marriage and then moves to a state that does not — or how such cross-state movements might affect the employment benefits those individuals are entitled to.

The Supreme Court’s 2012-2013 term made history by striking down key elements of the Voting Rights Act and the Defense of Marriage Act, both in 5 to 4 decisions. See how agreement on the court breaks down in this interactive graphic.

“You’re left with the dilemma of someone who marries in a state where it’s legal, and moves to another state [where it is not],” said Diane Thompson, an employee benefits lawyer at Ballard Spahr. “If they’re working for same employer, what does the employer do?”

Thousands of same-sex married couples will see their lives change in ways big and small because of the federal government’s recognition of them. A9