Does an employer with less than 100 participants have to file a Form 5500 if they make employer contributions to the employee's medical flex spending account?

Doesn't sound like it. The IRS does not require a Form 5500/Schedule F, and ERISA does not require one if you have fewer than 100 participants and are unfunded (no employee contributions).

What if both the employer and employee are making contributions to the account? Thanks!

Actually, ERISA Technical Release 92-01 allows pre-tax employee contributions to FSA's while allowing the plan to remain "unfunded." Since you have fewer than 100 participants and 92-01 keeps the plan unfunded, you don't have to file 5500.

I would be careful - I believe that it would depend on where the money is going. If you are depositing funds into a trust set up in the cafeteria plan's name, I think you have a filing requirement. If instead the money is going to the general assets of the employer or reimbursing claims, then you don't have a trust, are indeed unfunded, and therefore don't have a filing requirement.

Good point. That is correct. FSA checks need to be in the employer's name for the plan to stay "unfunded".

thank you