| 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 |
| 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 |
| 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 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 |
| Eisenhower FellowshipsEIN 23-1505095 | International | PA | $5,228,287Mid-sized | 94.38 |
| 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 |
| ElderHelp of San DiegoEIN 95-2880426 | Human Services | CA | $1,169,210Small | 92.85 |
| 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 |
| 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 Youth FoundationEIN 62-1474791 | Human Services | TN | $4,181,968Mid-sized | 90.73 |
| 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 |
| Emily K CenterEIN 56-2230469 | Human Services | NC | $2,219,274Small | 91.11 |
| EMpowerEIN 03-0529005 | International | NY | $4,505,664Mid-sized | 91.55 |
| Encore.orgEIN 94-3274339 | Research and Public Policy | CA | $6,224,565Mid-sized | 90.71 |
| Energy Outreach ColoradoEIN 74-2543881 | Human Services | CO | $25,022,578Large | 90.82 |
| Engineering Ministries InternationalEIN 74-2213629 | International | CO | $5,325,116Mid-sized | 94.27 |
| Ensemble Theater CompanyEIN 95-3408200 | Arts, Culture, Humanities | CA | $2,506,179Small | 90.58 |
| Enterprise Community PartnersEIN 52-1231931 | Community Development | MD | $67,947,685Large | 94.66 |
| Entertainment Industry FoundationEIN 95-1644609 | Health | CA | $61,723,094Large | 97.17 |
| EntrustEIN 54-1256309 | Religion | CO | $3,792,951Mid-sized | 93.47 |
| Environmental Advocates of New YorkEIN 22-2360736 | Environment | NY | $1,251,586Small | 99.79 |
| Environmental and Energy Study InstituteEIN 52-1268030 | Environment | DC | $1,296,571Small | 100.00 |
| Environmental Defense CenterEIN 77-0061994 | Environment | CA | $1,135,564Small | 90.57 |
| Environmental Grantmakers AssociationEIN 20-8817646 | Environment | NY | $2,539,563Small | 91.44 |
| Environmental InitiativeEIN 41-1718834 | Environment | MN | $2,064,185Small | 96.07 |
| Environmental Law Alliance WorldwideEIN 94-3116602 | Environment | OR | $1,816,495Small | 95.34 |
| Environmental Law and Policy CenterEIN 36-3866530 | Environment | IL | $6,344,275Mid-sized | 93.30 |
| Environmental Law InstituteEIN 52-0901863 | Environment | DC | $5,604,514Mid-sized | 92.44 |
| Environmental Research and Education FoundationEIN 52-1804051 | Environment | NC | $2,511,072Small | 95.50 |
| Environmental Working GroupEIN 52-2148600 | Environment | DC | $9,318,340Mid-sized | 91.51 |
| EOD Warrior FoundationEIN 20-8618412 | Human Services | FL | $1,378,932Small | 92.02 |
| Episcopal Relief & DevelopmentEIN 73-1635264 | International | NY | $21,968,901Large | 91.01 |
| Epworth Children's HomeEIN 57-0314389 | Human Services | SC | $6,948,186Mid-sized | 94.72 |
| Equal Justice InitiativeEIN 63-1135091 | Human and Civil Rights | AL | $5,690,202Mid-sized | 100.00 |
| Equal Justice WorksEIN 52-1469738 | Human and Civil Rights | DC | $17,605,902Large | 90.17 |
| Equality California InstituteEIN 68-0438008 | Human and Civil Rights | CA | $1,960,521Small | 90.71 |
| Equality Florida InstituteEIN 59-3435235 | Human and Civil Rights | FL | $2,652,749Small | 92.03 |
| Equality NowEIN 13-3660566 | International | NY | $4,916,223Mid-sized | 94.13 |
| Erie Community FoundationEIN 25-6032032 | Community Development | PA | $20,998,824Large | 96.64 |
| Española HumaneEIN 85-0406234 | Animals | NM | $1,802,326Small | 91.91 |
| EsperançaEIN 23-7087997 | International | AZ | $3,551,448Mid-sized | 94.64 |
| ETV Endowment of South CarolinaEIN 57-0657549 | Arts, Culture, Humanities | SC | $7,062,134Mid-sized | 96.42 |
| Eva's Village, Inc.EIN 22-2424542 | Human Services | NJ | $11,009,934Mid-sized | 95.49 |
| Evans Scholars FoundationEIN 36-2518129 | Education | IL | $27,629,028Large | 92.67 |