Amit Rakhit earns the same salary as other vice presidents leading drug development teams at the Weston-based biotech company Biogen Idec, but, because he is gay, he ends up bringing home about $3,000 less every year. Unlike his married heterosexual co-workers, Rakhit, 42, is taxed on income that goes toward his husband’s health insurance plan; for other spouses, that money is tax-free.

Even in states like Massachusetts where gay marriage is legal, same-sex spouses don’t get a tax break from Uncle Sam on medical, dental, and vision insurance because gay marriage isn’t recognized under federal law. Starting Jan. 1, Biogen Idec will begin addressing this inequity, joining just a few dozen companies in the United States that offer a similar type of reimbursement, including three based in Massachusetts.