The penalty for late filing of Form 5558 varies depending on the circumstances. Generally, the penalty for filing a late Form 5558 is $50 for each month or part of a month the form is late, multiplied by the total number of individuals or participants the Form 5558 pertains to. However, the penalty can be reduced or waived if the delay in filing was due to reasonable cause and not willful neglect. It is advisable to consult with a tax professional or refer to the instructions of Form 5558 for specific penalties and provisions in your situation.