| 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 |
| Emily K CenterEIN 56-2230469 | Human Services | NC | $2,219,274Small | 91.11 |
| Emmaus H.O.M.E.EIN 01-0287624 | Community Development | ME | $1,561,527Small | 72.60 |
| EMpowerEIN 03-0529005 | International | NY | $4,505,664Mid-sized | 91.55 |
| Empowering Lives InternationalEIN 33-0610787 | International | CA | $1,459,122Small | 79.89 |
| 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 |
| Encore.orgEIN 94-3274339 | Research and Public Policy | CA | $6,224,565Mid-sized | 90.71 |
| enCourage Kids FoundationEIN 13-3442216 | Health | NY | $3,110,680Small | 89.25 |
| EndeavorEIN 13-3931449 | International | NY | $9,653,170Mid-sized | 89.63 |
| Endometriosis AssociationEIN 39-1414754 | Health | WI | $337,741Small | 73.20 |
| endPoverty.orgEIN 54-1371549 | International | VA | $501,476Small | 76.19 |
| Energy Outreach ColoradoEIN 74-2543881 | Human Services | CO | $25,022,578Large | 90.82 |
| EngenderHealthEIN 13-1623838 | International | DC | $61,909,568Large | 88.50 |
| Engineering Ministries InternationalEIN 74-2213629 | International | CO | $5,325,116Mid-sized | 94.27 |
| English Language Institute/ChinaEIN 95-3551085 | International | CO | $18,429,283Large | 80.10 |
| Enlace ChicagoEIN 36-3727669 | Community Development | IL | $3,830,895Mid-sized | 88.22 |
| ENLACE USAEIN 04-3675191 | International | CA | $1,701,249Small | 81.89 |
| 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 |