| Samaritan HouseEIN 23-7416272 | Human Services | CA | $10,205,305Mid-sized | 94.93 |
| San Diego Botanic GardenEIN 95-6120581 | Environment | CA | $2,978,807Small | 84.42 |
| San Diego Center for the BlindEIN 95-3076944 | Health | CA | $1,712,478Small | 94.05 |
| San Diego Children's Discovery MuseumEIN 33-0912735 | Arts, Culture, Humanities | CA | $1,516,896Small | 91.02 |
| San Diego CoastkeeperEIN 33-0647946 | Environment | CA | $668,734Small | 78.81 |
| San Diego Habitat for HumanityEIN 33-0259190 | Community Development | CA | $10,957,226Mid-sized | 92.92 |
| San Diego History CenterEIN 95-1728991 | Arts, Culture, Humanities | CA | $2,750,444Small | 80.20 |
| 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 |
| 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 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 |
| Scholarship Foundation of Santa BarbaraEIN 23-7087774 | Education | CA | $10,071,712Mid-sized | 91.88 |
| School on WheelsEIN 95-4422640 | Education | CA | $2,114,477Small | 95.47 |
| Scleroderma Research FoundationEIN 68-0087234 | Health | CA | $2,527,636Small | 97.17 |
| Second Harvest Food Bank of Orange CountyEIN 32-0362611 | Human Services | CA | $53,968,186Large | 96.80 |
| Second Harvest Food Bank of Santa Clara and San Mateo CountiesEIN 94-2614101 | Human Services | CA | $125,127,781Large | 97.68 |
| Second Harvest Food Bank Santa Cruz CountyEIN 77-0326685 | Human Services | CA | $19,193,561Large | 92.74 |
| Segerstrom Center for the ArtsEIN 23-7287150 | Arts, Culture, Humanities | CA | $69,295,404Large | 89.82 |
| Senior ConcernsEIN 95-2992927 | Human Services | CA | $1,864,713Small | 84.52 |
| SETI InstituteEIN 94-2951356 | Research and Public Policy | CA | $20,609,248Large | 87.01 |
| Seva FoundationEIN 38-2231279 | International | CA | $7,518,689Mid-sized | 92.27 |
| SFFILMEIN 94-2663216 | Arts, Culture, Humanities | CA | $6,042,427Mid-sized | 87.22 |