| 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 |
| ECAD, Educated Canines Assisting with DisabilitiesEIN 06-1436718 | Animals | CT | $895,834Small | 92.92 |
| ECHOEIN 23-7275283 | International | FL | $4,125,712Mid-sized | 95.27 |
| ECHO (Everyone Cooperating to Help Others)EIN 39-1222279 | Human Services | WI | $2,388,786Small | 92.59 |
| ECHO Lake Aquarium and Science CenterEIN 03-0347288 | Arts, Culture, Humanities | VT | $3,464,446Small | 91.45 |
| ECHO of BrandonEIN 59-3051533 | Human Services | FL | $1,536,158Small | 78.95 |
| ecoAmericaEIN 20-3895611 | Environment | DC | $4,482,513Mid-sized | 88.77 |
| EcoHealth AllianceEIN 31-1726494 | Animals | NY | $13,652,783Large | 92.92 |
| EcoLogic Development FundEIN 25-1704582 | Environment | MA | $1,487,137Small | 81.51 |
| Ecology CenterEIN 38-1912803 | Environment | MI | $1,941,562Small | 93.09 |
| Economic Policy InstituteEIN 52-1368964 | Research and Public Policy | DC | $6,502,386Mid-sized | 90.38 |
| EcoTariumEIN 04-2105868 | Arts, Culture, Humanities | MA | $4,965,747Mid-sized | 88.48 |
| EcotrustEIN 93-1050144 | Environment | OR | $5,895,078Mid-sized | 88.19 |
| Ecumenical Hunger ProgramEIN 94-2476942 | Human Services | CA | $5,283,069Mid-sized | 98.23 |
| EdChoiceEIN 35-1978359 | Education | IN | $7,685,637Mid-sized | 92.71 |
| Edgar Cayce's A.R.E.EIN 54-0573802 | Human Services | VA | $7,633,709Mid-sized | 86.67 |
| Edgewood Children's RanchEIN 59-1150182 | Human Services | FL | $1,868,366Small | 93.28 |
| EdifyEIN 27-0892545 | Religion | CA | $5,393,592Mid-sized | 90.90 |
| Edith and Carl Marks Jewish Community House of BensonhurstEIN 11-1633484 | Human Services | NY | $9,407,466Mid-sized | 91.97 |
| Educando by WorldfundEIN 03-0483824 | International | DC | $2,874,579Small | 94.18 |
| Education For EmploymentEIN 82-0578781 | Education | DC | $5,167,691Mid-sized | 90.31 |
| Education Foundation of Palm Beach CountyEIN 59-2420369 | Education | FL | $2,400,649Small | 92.92 |
| Education Law CenterEIN 22-2014555 | Human and Civil Rights | NJ | $1,953,793Small | 85.06 |
| Education PioneersEIN 77-0602311 | Education | CA | $8,576,514Mid-sized | 72.24 |
| Education Through Music, Inc. (New York)EIN 13-3613210 | Education | NY | $4,975,061Mid-sized | 93.96 |
| Education Writers AssociationEIN 23-7439790 | Education | DC | $2,594,778Small | 90.26 |
| Educational First StepsEIN 75-2334053 | Education | TX | $3,752,714Mid-sized | 95.61 |
| Educational Media FoundationEIN 94-2816342 | Religion | CA | $112,676,029Large | 94.34 |
| 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 |
| Eisenhower FellowshipsEIN 23-1505095 | International | PA | $5,228,287Mid-sized | 94.38 |
| Eisenhower FoundationEIN 48-0634284 | Arts, Culture, Humanities | KS | $2,432,358Small | 77.15 |
| 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 Buen SamaritanoEIN 74-2488682 | Human Services | TX | $6,467,481Mid-sized | 92.31 |
| El Hogar MinistriesEIN 04-3580644 | International | MA | $1,498,436Small | 91.26 |
| El Museo del BarrioEIN 23-7156720 | Arts, Culture, Humanities | NY | $3,296,157Small | 74.33 |
| El Paso Community FoundationEIN 74-1839536 | Community Development | TX | $10,840,264Mid-sized | 88.76 |
| ElderHelp of San DiegoEIN 95-2880426 | Human Services | CA | $1,169,210Small | 92.85 |
| Ele's PlaceEIN 38-2976751 | Human Services | MI | $2,794,372Small | 87.66 |
| Electronic Frontier FoundationEIN 04-3091431 | Human and Civil Rights | CA | $11,398,529Mid-sized | 95.96 |
| Electronic Privacy Information CenterEIN 52-2225921 | Human and Civil Rights | DC | $1,523,199Small | 97.17 |
| ELEM/Youth in Distress in IsraelEIN 13-3171815 | Human Services | NY | $888,375Small | 74.55 |
| 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 |
| Elton John AIDS FoundationEIN 58-2033460 | Health | NY | $10,028,552Mid-sized | 95.12 |
| ElunaEIN 91-2065051 | Human Services | PA | $2,819,395Small | 91.13 |
| Emerald Coast Children's Advocacy CenterEIN 59-3454168 | Human Services | FL | $1,242,926Small | 90.70 |
| Emerald Necklace ConservancyEIN 04-3414988 | Environment | MA | $1,687,443Small | 83.01 |
| Emerald Youth FoundationEIN 62-1474791 | Human Services | TN | $4,181,968Mid-sized | 90.73 |
| Emergency Family Assistance AssociationEIN 84-0454115 | Human Services | CO | $4,325,753Mid-sized | 88.34 |
| Emergency Food NetworkEIN 94-3131776 | Human Services | WA | $23,422,846Large | 91.78 |
| Emergency Infant ServicesEIN 73-1039524 | Human Services | OK | $3,126,481Small | 95.47 |
| Emergency Medicine FoundationEIN 75-2331221 | Health | TX | $2,548,384Small | 94.34 |