What is the difference between direct and indirect expenses on Form 990 PF?
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Direct Expenses are expenses that are directly involved in particular business activities. Those are, 

• Compensation and travel expenses
• The cost of materials and supplies utilized 
• Fees paid to outside firms and individuals in connection with a business activity 

 
Expenses that are not directly involved in a particular business activity but are related to the direct costs incurred in conducting that activity are called Indirect expenses. Those are, 
Occupancy expenses 

• Supervisory and clerical compensation
• Repair, Rental, and Maintenance of equipment
• Expenses incurred by other departments or cost centers that support the department or function responsible for the direct expenses associated with an activity
• Other applicable general and administrative expenses.