| Dollywood FoundationEIN 62-1348105 | Education | TN | $2,763,686Small | 84.26 |
| Domestic Violence Center of Chester CountyEIN 22-2606511 | Human Services | PA | $1,767,014Small | 88.49 |
| Domestic Violence ProjectEIN 34-1263226 | Human Services | OH | $1,759,397Small | 86.59 |
| Domestic Violence Solutions for Santa Barbara CountyEIN 95-3495141 | Human Services | CA | $1,830,345Small | 84.41 |
| Donald W. Reynolds Boys & Girls ClubEIN 71-0254287 | Human Services | AR | $2,246,524Small | 88.23 |
| Doug Flutie Jr. Foundation For AutismEIN 04-3543134 | Health | MA | $1,281,666Small | 87.31 |
| DoveLewis Emergency Animal HospitalEIN 93-0621534 | Animals | OR | $12,932,704Mid-sized | 86.84 |
| Downline MinistriesEIN 20-1374884 | Religion | TN | $1,631,991Small | 80.75 |
| Downtown Cleveland AllianceEIN 34-1775903 | Community Development | OH | $7,152,083Mid-sized | 81.88 |
| Downtown Women's CenterEIN 31-1597223 | Human Services | CA | $10,092,147Mid-sized | 89.78 |
| DreamYard ProjectEIN 13-3759661 | Education | NY | $5,082,563Mid-sized | 86.67 |
| Drugs for Neglected Diseases Initiative North AmericaEIN 20-8774179 | Health | NY | $4,091,229Mid-sized | 84.44 |
| Dubuque Regional Humane SocietyEIN 42-6039535 | Animals | IA | $1,228,456Small | 83.90 |
| DuPage Children's MuseumEIN 36-3565001 | Arts, Culture, Humanities | IL | $3,932,978Mid-sized | 84.78 |
| Dutchess County SPCAEIN 14-1340058 | Animals | NY | $2,016,618Small | 85.23 |
| Dysautonomia FoundationEIN 13-6145280 | Health | NY | $2,427,386Small | 85.38 |
| Eagles Charitable FoundationEIN 23-2794290 | Human Services | PA | $1,448,292Small | 84.23 |
| Earth ForceEIN 52-1830873 | Environment | CO | $1,002,263Small | 84.00 |
| Earth Island InstituteEIN 94-2889684 | Environment | CA | $9,751,020Mid-sized | 88.24 |
| EarthEcho InternationalEIN 95-4789334 | Environment | DC | $698,764Small | 82.66 |
| EarthplaceEIN 06-0740523 | Environment | CT | $2,425,838Small | 85.32 |
| EarthShare GeorgiaEIN 58-2022001 | Environment | GA | $635,892Small | 80.68 |
| EarthShare TexasEIN 74-2627643 | Environment | TX | $407,224Small | 84.86 |
| Earthwatch InstituteEIN 23-7168440 | Research and Public Policy | MA | $7,458,378Mid-sized | 86.99 |
| East Bay Community FoundationEIN 94-6070996 | Community Development | CA | $29,631,756Large | 87.62 |
| East Bay SPCAEIN 94-1322202 | Animals | CA | $10,413,347Mid-sized | 89.81 |
| East End HouseEIN 04-2104163 | Human Services | MA | $2,610,655Small | 80.06 |
| East Lake FoundationEIN 58-2204306 | Community Development | GA | $16,362,404Large | 89.24 |
| East Texas Crisis CenterEIN 75-1641173 | Human Services | TX | $2,141,385Small | 86.52 |
| East-West Center FoundationEIN 99-0218752 | International | HI | $819,979Small | 83.27 |
| Eastern Market CorporationEIN 32-0030432 | Community Development | MI | $5,687,857Mid-sized | 89.99 |
| Eastern Music FestivalEIN 56-0771005 | Arts, Culture, Humanities | NC | $2,334,231Small | 81.51 |
| Eastside Baby CornerEIN 91-1617032 | Human Services | WA | $7,561,571Mid-sized | 88.14 |
| Ebenezer Christian Children's HomeEIN 56-1861709 | Human Services | NC | $2,295,078Small | 82.89 |
| Eblen CharitiesEIN 56-1758077 | Health | NC | $4,928,118Mid-sized | 86.29 |
| ecoAmericaEIN 20-3895611 | Environment | DC | $4,482,513Mid-sized | 88.77 |
| EcoLogic Development FundEIN 25-1704582 | Environment | MA | $1,487,137Small | 81.51 |
| EcoTariumEIN 04-2105868 | Arts, Culture, Humanities | MA | $4,965,747Mid-sized | 88.48 |
| EcotrustEIN 93-1050144 | Environment | OR | $5,895,078Mid-sized | 88.19 |
| Edgar Cayce's A.R.E.EIN 54-0573802 | Human Services | VA | $7,633,709Mid-sized | 86.67 |
| Education Law CenterEIN 22-2014555 | Human and Civil Rights | NJ | $1,953,793Small | 85.06 |
| EdVentureEIN 57-1013857 | Arts, Culture, Humanities | SC | $4,782,439Mid-sized | 86.39 |
| EdVestorsEIN 76-0794873 | Education | MA | $3,232,210Small | 84.68 |
| EFRAT-C.R.I.B. Committee for the Rescue of Israel's BabiesEIN 22-3431457 | Human Services | NY | $2,588,353Small | 86.13 |
| Eiteljorg Museum of American Indians and Western ArtEIN 31-1139447 | Arts, Culture, Humanities | IN | $9,127,483Mid-sized | 84.73 |
| Ekal Vidyalaya Foundation of USAEIN 77-0554248 | Education | TX | $8,661,375Mid-sized | 87.74 |
| El Paso Community FoundationEIN 74-1839536 | Community Development | TX | $10,840,264Mid-sized | 88.76 |
| Ele's PlaceEIN 38-2976751 | Human Services | MI | $2,794,372Small | 87.66 |
| Elie Wiesel Foundation for HumanityEIN 13-3398151 | International | NY | $1,039,897Small | 80.59 |
| Elijah's PromiseEIN 22-3055539 | Human Services | NJ | $2,160,208Small | 89.02 |
| Elizabeth Glaser Pediatric AIDS FoundationEIN 95-4191698 | Health | DC | $180,014,269Large | 88.29 |
| Elk Grove Food Bank ServicesEIN 38-3664737 | Human Services | CA | $2,664,368Small | 83.01 |
| Elmbrook Humane SocietyEIN 39-6091712 | Animals | WI | $1,164,047Small | 89.63 |
| Elmwood Park ZooEIN 23-1970067 | Animals | PA | $6,775,573Mid-sized | 89.94 |
| Emerald Necklace ConservancyEIN 04-3414988 | Environment | MA | $1,687,443Small | 83.01 |
| Emergency Family Assistance AssociationEIN 84-0454115 | Human Services | CO | $4,325,753Mid-sized | 88.34 |
| Emunah of AmericaEIN 13-2670365 | Human Services | NY | $5,123,297Mid-sized | 82.55 |
| EnactusEIN 74-2148471 | Education | MO | $14,501,666Large | 82.89 |
| EncompassEIN 91-0825232 | Human Services | WA | $3,883,177Mid-sized | 89.50 |
| enCourage Kids FoundationEIN 13-3442216 | Health | NY | $3,110,680Small | 89.25 |