| San Diego Humane Society EIN 95-1661688 | Animals | CA | $25,491,250Large | 92.49 |
| 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 Rescue MissionEIN 95-1874073 | Human Services | CA | $19,785,817Large | 86.04 |
| San Diego River Park FoundationEIN 01-0565671 | Environment | CA | $939,333Small | 85.40 |
| San Diego Second Chance ProgramEIN 33-0539640 | Human Services | CA | $6,021,277Mid-sized | 87.55 |
| San Diego Symphony OrchestraEIN 95-2040874 | Arts, Culture, Humanities | CA | $26,040,490Large | 93.01 |
| San Diego Zoo GlobalEIN 95-1648219 | Animals | CA | $263,690,859Large | 92.36 |
| San Francisco AIDS FoundationEIN 94-2927405 | Health | CA | $31,653,409Large | 92.19 |
| San Francisco BalletEIN 94-1415298 | Arts, Culture, Humanities | CA | $50,771,268Large | 82.83 |
| San Francisco BaykeeperEIN 68-0120240 | Environment | CA | $1,512,332Small | 84.75 |
| San Francisco Botanical Garden SocietyEIN 94-6050168 | Environment | CA | $4,261,791Mid-sized | 92.52 |
| San Francisco CASAEIN 94-3039028 | Human Services | CA | $1,314,905Small | 92.51 |
| San Francisco Education FundEIN 94-1592822 | Education | CA | $2,439,113Small | 97.17 |
| San Francisco Gay Men's ChorusEIN 94-2576101 | Arts, Culture, Humanities | CA | $2,592,794Small | 79.95 |
| San Francisco Girls ChorusEIN 94-2711726 | Education | CA | $1,869,096Small | 79.41 |
| San Francisco Museum of Modern ArtEIN 94-1156300 | Arts, Culture, Humanities | CA | $86,111,301Large | 85.61 |
| San Francisco OperaEIN 94-0836240 | Arts, Culture, Humanities | CA | $77,826,840Large | 87.05 |
| San Francisco Parks AllianceEIN 23-7131784 | Environment | CA | $15,142,255Large | 92.48 |
| San Francisco PerformancesEIN 94-2600147 | Arts, Culture, Humanities | CA | $3,233,850Small | 88.79 |
| San Francisco SPCAEIN 94-0836580 | Animals | CA | $37,358,567Large | 95.47 |
| San Francisco ZooEIN 94-1429538 | Animals | CA | $24,928,934Large | 84.00 |
| San Gabriel Valley Habitat for HumanityEIN 95-4244947 | Community Development | CA | $4,289,122Mid-sized | 100.00 |
| San Joaquin River Parkway and Conservation TrustEIN 77-0196692 | Environment | CA | $1,749,897Small | 90.56 |
| San Jose Museum of ArtEIN 23-7062028 | Arts, Culture, Humanities | CA | $4,586,772Mid-sized | 89.14 |
| San Luis Obispo SymphonyEIN 95-2493144 | Arts, Culture, Humanities | CA | $1,134,318Small | 76.61 |
| Sanctuary for FamiliesEIN 13-3193119 | Human Services | NY | $21,026,926Large | 92.24 |
| Sandusky State TheaterEIN 34-1568622 | Arts, Culture, Humanities | OH | $1,008,488Small | 72.56 |
| Sanibel-Captiva Conservation FoundationEIN 59-1205087 | Environment | FL | $3,095,476Small | 90.45 |
| Sankara Eye Foundation, USAEIN 77-6141976 | Health | CA | $7,330,498Mid-sized | 100.00 |
| Sankara Nethralaya Om TrustEIN 52-1611548 | Health | MD | $912,982Small | 86.07 |
| 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 FoundationEIN 95-1866094 | Community Development | CA | $32,703,267Large | 95.50 |
| Santa Barbara Historical MuseumEIN 95-6005796 | Arts, Culture, Humanities | CA | $1,580,925Small | 85.57 |
| 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 Neighborhood ClinicsEIN 77-0496382 | Health | CA | $14,396,726Large | 91.45 |
| Santa Barbara Opera AssociationEIN 77-0347413 | Arts, Culture, Humanities | CA | $1,636,380Small | 72.64 |
| Santa Barbara Rescue MissionEIN 95-6134271 | Human Services | CA | $2,671,065Small | 83.81 |
| Santa Barbara Symphony Orchestra AssociationEIN 95-2104089 | Arts, Culture, Humanities | CA | $3,200,471Small | 87.97 |
| Santa Barbara ZooEIN 95-2268554 | Animals | CA | $11,444,973Mid-sized | 93.81 |
| Santa Cruz Museum of Art and History at the McPherson CenterEIN 94-2718861 | Arts, Culture, Humanities | CA | $1,864,470Small | 92.02 |
| Santa Fe Animal Shelter & Humane SocietyEIN 85-6000484 | Animals | NM | $7,928,140Mid-sized | 90.45 |
| Santa Fe Art InstituteEIN 85-0404277 | Arts, Culture, Humanities | NM | $775,980Small | 83.63 |
| Santa Fe Chamber Music FestivalEIN 85-0224461 | Arts, Culture, Humanities | NM | $2,360,562Small | 82.12 |
| Santa Fe InstituteEIN 85-0325494 | Research and Public Policy | NM | $10,668,030Mid-sized | 84.43 |
| Sarah's CircleEIN 36-3043662 | Human Services | IL | $2,023,629Small | 92.21 |
| 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 |
| Sarcoma Foundation of AmericaEIN 52-2275294 | Health | MD | $1,903,735Small | 94.74 |
| 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 Jewish FederationEIN 58-0566231 | Community Development | GA | $2,108,440Small | 94.04 |
| Savannah Music FestivalEIN 58-1401616 | Arts, Culture, Humanities | GA | $3,604,074Mid-sized | 85.71 |
| Save a Child's Heart FoundationEIN 52-1783323 | International | MD | $2,474,430Small | 96.16 |
| Save Our Wild SalmonEIN 91-1673170 | Animals | WA | $219,201Small | 77.10 |