| University of Rochester | $6,415,541,241 |
| Rochester General Hospital | $1,742,626,515 |
| Rochester Institute of Technology | $1,173,696,705 |
| The Unity Hospital of Rochester | $717,211,967 |
| Highland Hospital of Rochester | $614,517,494 |
| St John Fisher University | $183,894,801 |
| United Memorial Medical Center | $180,136,139 |
| Heritage Christian Services Inc | $165,678,735 |
| Hillside Childrens Center | $144,254,396 |
| Clifton Springs Sanitarium Co | $140,255,689 |
| Nazareth University | $140,046,461 |
| Western New York Medical Practice PC | $132,182,840 |
| Newark Wayne Community Hospital | $127,744,315 |
| Catholic Charities of the Diocese of Rochester | $120,379,765 |
| Lifetime Assistance Incorporated | $108,886,578 |
| Independent Living for Seniors Inc | $101,451,446 |
| Genesee Region Home Care Association Inc | $84,247,250 |
| Trillium Health Inc | $77,899,629 |
| St Anns Home for the Aged | $75,138,215 |
| YMCA of Greater Rochester | $71,624,858 |
| Rochester Area Community Foundation | $64,764,956 |
| Jewish Home of Rochester | $64,759,331 |
| Roberts Wesleyan University | $62,623,063 |
| Goodwill of the Finger Lakes Inc | $56,612,578 |
| Center for Disability Rights Inc | $56,069,244 |
| Pathstone Corporation | $50,960,569 |
| Rochester Regional Health | $48,445,192 |
| Grhs Foundation Inc | $44,306,330 |
| United Way of Greater Rochester and the Finger Lakes Inc | $31,752,740 |
| Esl Charitable Foundation Inc | $28,600,563 |
| Max and Marian Farash Charitable Foundation | $26,460,451 |
| Pathstone Corporation | $22,720,847 |
| Margaret Woodbury Strong Museum | $22,452,727 |
| Greater Rochester Health Foundation | $10,581,311 |