| Samaritan's FeetEIN 14-1880905 | International | NC | $7,532,515Mid-sized | 92.38 |
| SAMMinistriesEIN 74-2285793 | Human Services | TX | $11,377,425Mid-sized | 86.35 |
| San Angelo Area FoundationEIN 73-1634145 | Community Development | TX | $9,025,193Mid-sized | 91.42 |
| San Antonio Humane SocietyEIN 74-6024105 | Animals | TX | $4,354,685Mid-sized | 95.34 |
| San Antonio Museum of ArtEIN 74-2689943 | Arts, Culture, Humanities | TX | $9,370,712Mid-sized | 82.54 |
| San Diego Habitat for HumanityEIN 33-0259190 | Community Development | CA | $10,957,226Mid-sized | 92.92 |
| San Diego Museum of ArtEIN 95-1696715 | Arts, Culture, Humanities | CA | $12,653,010Mid-sized | 90.46 |
| San Diego Museum of ManEIN 95-1709290 | Arts, Culture, Humanities | CA | $4,304,545Mid-sized | 93.36 |
| San Diego Natural History MuseumEIN 95-1643375 | Arts, Culture, Humanities | CA | $11,738,954Mid-sized | 88.29 |
| San Diego Repertory TheatreEIN 95-3032308 | Arts, Culture, Humanities | CA | $4,625,627Mid-sized | 73.24 |
| San Diego Second Chance ProgramEIN 33-0539640 | Human Services | CA | $6,021,277Mid-sized | 87.55 |
| San Francisco Botanical Garden SocietyEIN 94-6050168 | Environment | CA | $4,261,791Mid-sized | 92.52 |
| San Gabriel Valley Habitat for HumanityEIN 95-4244947 | Community Development | CA | $4,289,122Mid-sized | 100.00 |
| San Jose Museum of ArtEIN 23-7062028 | Arts, Culture, Humanities | CA | $4,586,772Mid-sized | 89.14 |
| Sankara Eye Foundation, USAEIN 77-6141976 | Health | CA | $7,330,498Mid-sized | 100.00 |
| Sansum Diabetes Research InstituteEIN 95-1684086 | Health | CA | $3,554,163Mid-sized | 79.94 |
| Santa Barbara Botanic GardenEIN 95-1644628 | Environment | CA | $3,907,707Mid-sized | 90.80 |
| Santa Barbara Bowl FoundationEIN 95-3618955 | Arts, Culture, Humanities | CA | $5,722,096Mid-sized | 89.24 |
| Santa Barbara Museum of ArtEIN 95-1664122 | Arts, Culture, Humanities | CA | $8,480,089Mid-sized | 92.24 |
| Santa Barbara Museum of Natural HistoryEIN 95-1643378 | Arts, Culture, Humanities | CA | $7,363,122Mid-sized | 88.67 |
| Santa Barbara ZooEIN 95-2268554 | Animals | CA | $11,444,973Mid-sized | 93.81 |
| Santa Fe Animal Shelter & Humane SocietyEIN 85-6000484 | Animals | NM | $7,928,140Mid-sized | 90.45 |
| Santa Fe InstituteEIN 85-0325494 | Research and Public Policy | NM | $10,668,030Mid-sized | 84.43 |
| Sarasota OperaEIN 23-7089047 | Arts, Culture, Humanities | FL | $8,600,781Mid-sized | 86.80 |
| Sarasota OrchestraEIN 59-2603081 | Arts, Culture, Humanities | FL | $9,770,009Mid-sized | 90.31 |
| Sargent Shriver National Center on Poverty LawEIN 36-3151279 | Human and Civil Rights | IL | $5,797,979Mid-sized | 92.18 |
| SAT-7EIN 23-2964829 | Religion | MD | $9,134,848Mid-sized | 82.79 |
| Savannah Music FestivalEIN 58-1401616 | Arts, Culture, Humanities | GA | $3,604,074Mid-sized | 85.71 |
| Save the FamilyEIN 86-0665712 | Human Services | AZ | $5,414,265Mid-sized | 81.68 |
| SBH Community Service NetworkEIN 23-7406410 | Human Services | NY | $9,752,470Mid-sized | 96.54 |
| Scholarship Foundation of Santa BarbaraEIN 23-7087774 | Education | CA | $10,071,712Mid-sized | 91.88 |
| Scholarship Foundation of St. LouisEIN 43-6031234 | Education | MO | $6,200,105Mid-sized | 87.18 |
| Scholastic Art & Writing AwardsEIN 13-3780998 | Education | NY | $3,826,838Mid-sized | 81.28 |
| School for Advanced ResearchEIN 85-0125045 | Education | NM | $3,536,710Mid-sized | 88.22 |
| Science Center of IowaEIN 42-6097912 | Arts, Culture, Humanities | IA | $7,395,900Mid-sized | 88.53 |
| Science Museum OklahomaEIN 73-0682415 | Arts, Culture, Humanities | OK | $10,733,779Mid-sized | 96.87 |
| Scleroderma FoundationEIN 52-1375827 | Health | MA | $5,211,320Mid-sized | 96.52 |
| SCORE InternationalEIN 58-1605736 | Religion | TN | $8,470,138Mid-sized | 82.33 |
| Scott County Family YEIN 42-0703278 | Human Services | IA | $10,300,667Mid-sized | 93.54 |
| Scottsdale Cultural CouncilEIN 86-0593786 | Arts, Culture, Humanities | AZ | $11,500,947Mid-sized | 82.14 |
| Sea Education AssociationEIN 04-2702102 | Education | MA | $8,416,413Mid-sized | 83.40 |
| SeaGate Food BankEIN 51-0252948 | Human Services | OH | $6,481,656Mid-sized | 88.83 |
| Seattle Children's TheatreEIN 51-0172421 | Arts, Culture, Humanities | WA | $6,887,908Mid-sized | 86.49 |
| Seattle HumaneEIN 91-0282060 | Animals | WA | $6,703,024Mid-sized | 89.34 |
| Second Amendment FoundationEIN 91-6184167 | Human and Civil Rights | WA | $4,129,021Mid-sized | 74.92 |
| Second ChanceEIN 52-2276640 | Education | MD | $8,034,442Mid-sized | 85.43 |
| Second Harvest Community Food BankEIN 43-1268319 | Human Services | MO | $10,909,604Mid-sized | 93.83 |
| Second Harvest Food Bank of North Central OhioEIN 34-1446685 | Human Services | OH | $11,486,199Mid-sized | 96.94 |
| Second Harvest Northern Lakes Food BankEIN 36-3479964 | Human Services | MN | $10,915,737Mid-sized | 94.46 |
| Second HelpingsEIN 35-1484281 | Human Services | IN | $6,711,056Mid-sized | 98.23 |
| Second Stage TheatreEIN 13-3021180 | Arts, Culture, Humanities | NY | $9,254,856Mid-sized | 77.08 |
| SECOREIN 20-4226894 | Human Services | CO | $4,048,217Mid-sized | 72.61 |
| Securing America's Future EnergyEIN 20-1727977 | Research and Public Policy | DC | $6,080,643Mid-sized | 74.06 |
| Sedgwick County Zoological SocietyEIN 48-6120530 | Animals | KS | $11,658,916Mid-sized | 90.32 |
| Seed Savers ExchangeEIN 43-1214133 | Environment | IA | $5,385,772Mid-sized | 84.73 |
| Seeds of PeaceEIN 52-1814447 | International | NY | $5,723,593Mid-sized | 79.84 |
| Senator John Heinz History Center- Historical Society of Western PennsylvaniaEIN 25-0965391 | Arts, Culture, Humanities | PA | $11,115,252Mid-sized | 90.62 |
| Seneca Park Zoo SocietyEIN 16-0905390 | Animals | NY | $5,429,091Mid-sized | 81.24 |
| Senior NeighborsEIN 23-7195491 | Human Services | MI | $3,594,979Mid-sized | 94.69 |
| Senior ServicesEIN 56-1085968 | Human Services | NC | $6,935,007Mid-sized | 95.38 |