We have an employee going on disability leave in late December who has also elected the Flex Spending Account for 2009. We will not be able to deduct any of the pretax contributions since their will not be a paycheck in 2009 (while the employee is on leave). Should the employee pay us with after tax dollars (check) so they can access the entire annual election for 2009? They probably will return to work in March.

Check out Treas Reg §1.125-3, A-3(a) for descriptions of three allowable options: Pre-pay, Pay-as-you-go, or Catch-up options for payment. Even if the disability leave is not FMLA leave, this might be a good practice to use if your plan document doesn't specify something else