Your company is required to file Form 1099-MISC for each person you paid rents of at least $600 during the year. There are, however, certain exceptions where some payments do not have to be reported on Form 1099-MISC. Generally, any payments made to a C corporation, S corporation, or an LLC treated as either a C or S corporation, are exempt from reporting. In addition, payments to a tax exempt organization are also exempt from reporting. You should request the non-profit organization complete and sign a Form W-9 which certifies its tax exempt status. You can certainly report the rents if you wish, but you are not obligated to report rents or other payments to tax exempt organizations.