| Name | What | Region | Country | Lat | Long | Elev Ft. | Pop Est |
| Saga | city | Nagasaki-ken | Japan | 34.4522222 | 129.3702778 | 65 | 30224 |
| Saganoshima | city | Nagasaki-ken | Japan | 32.7166667 | 128.6 | 3 | 4792 |
| Saganoshimago | city | Nagasaki-ken | Japan | 32.7166667 | 128.6 | 3 | 4792 |
| Saganoshimagō | city | Nagasaki-ken | Japan | 32.7166667 | 128.6 | 3 | 4792 |
| Sago | city | Nagasaki-ken | Japan | 34.6166667 | 129.35 | 144 | 28618 |
| Saho | city | Nagasaki-ken | Japan | 34.4 | 129.2833333 | 311 | 15621 |
| Saishi | city | Nagasaki-ken | Japan | 33.2 | 129.7166667 | 278 | 36243 |
| Saisni | city | Nagasaki-ken | Japan | 33.2 | 129.7166667 | 278 | 36243 |
| Saka | city | Nagasaki-ken | Japan | 34.4522222 | 129.3702778 | 65 | 30224 |
| Sakakinoura | city | Nagasaki-ken | Japan | 32.8883333 | 129.0166667 | 275 | 21978 |
| Sakihario | city | Nagasaki-ken | Japan | 33.05 | 129.7666667 | 0 | 21239 |
| Sakito | city | Nagasaki-ken | Japan | 33 | 129.55 | 0 | 3798 |
| Sakiyama | city | Nagasaki-ken | Japan | 32.65 | 128.8833333 | 95 | 8437 |
| Sanri | city | Nagasaki-ken | Japan | 33.4 | 129.7333333 | 0 | 10544 |
| Sao | city | Nagasaki-ken | Japan | 32.8166667 | 129.05 | 0 | 7337 |
| Sasa | city | Nagasaki-ken | Japan | 33.2333333 | 129.65 | 150 | 34494 |
| Sasebo | city | Nagasaki-ken | Japan | 33.1591667 | 129.7227778 | 0 | 27934 |
| Saseho | city | Nagasaki-ken | Japan | 33.1591667 | 129.7227778 | 0 | 27934 |
| Sasu | city | Nagasaki-ken | Japan | 34.2333333 | 129.2 | 295 | 19523 |
| Sasu | city | Nagasaki-ken | Japan | 34.2333333 | 129.2166667 | 282 | 33595 |
| Sasuna | city | Nagasaki-ken | Japan | 34.6333333 | 129.3922222 | 544 | 24142 |
| Sasuno | city | Nagasaki-ken | Japan | 34.6333333 | 129.3922222 | 544 | 24142 |
| Sasuse | city | Nagasaki-ken | Japan | 34.15 | 129.1833333 | 291 | 21080 |
| Sau | city | Nagasaki-ken | Japan | 34.4 | 129.2833333 | 311 | 15621 |
| Sazare | city | Nagasaki-ken | Japan | 32.8333333 | 128.85 | 0 | 13225 |
| Sechibaru | city | Nagasaki-ken | Japan | 33.25 | 129.75 | 931 | 40545 |
| Sechihara | city | Nagasaki-ken | Japan | 33.25 | 129.75 | 931 | 40545 |
| Sembon | city | Nagasaki-ken | Japan | 32.7 | 129.85 | 173 | 26476 |
| Sembonyama | city | Nagasaki-ken | Japan | 32.7 | 129.85 | 173 | 26476 |
| Seno | city | Nagasaki-ken | Japan | 32.7333333 | 130.3666667 | 3 | 27749 |
| Seto | city | Nagasaki-ken | Japan | 32.9333333 | 129.6333333 | 0 | 20685 |
| Shijiki | city | Nagasaki-ken | Japan | 33.2 | 129.4 | 3 | 13003 |
| Shikama | city | Nagasaki-ken | Japan | 32.9833333 | 129.65 | 190 | 22713 |
| Shikamachi | city | Nagasaki-ken | Japan | 33.2666667 | 129.5833333 | 167 | 17647 |
| Shikayama | city | Nagasaki-ken | Japan | 33.1333333 | 129.9 | 278 | 41030 |
| Shikimi | city | Nagasaki-ken | Japan | 32.7833333 | 129.7833333 | 3 | 14250 |
| Shimabara | city | Nagasaki-ken | Japan | 32.7833333 | 130.3666667 | 16 | 28934 |
| Shimo-kurosaki | city | Nagasaki-ken | Japan | 32.8333333 | 129.7166667 | 68 | 17274 |
| Shimo-otsu | city | Nagasaki-ken | Japan | 32.6833333 | 128.85 | 246 | 20893 |
| Shimo-ozu | city | Nagasaki-ken | Japan | 32.6833333 | 128.85 | 246 | 20893 |
| Shimo-sakiyamago | city | Nagasaki-ken | Japan | 32.65 | 128.8833333 | 95 | 8437 |
| Shimo-sakiyamagō | city | Nagasaki-ken | Japan | 32.65 | 128.8833333 | 95 | 8437 |
| Shimo-utagaura | city | Nagasaki-ken | Japan | 33.2666667 | 129.5833333 | 167 | 17647 |
| Shimo-ōtsu | city | Nagasaki-ken | Japan | 32.6833333 | 128.85 | 246 | 20893 |
| Shimo-ōzu | city | Nagasaki-ken | Japan | 32.6833333 | 128.85 | 246 | 20893 |
| Shimogurosaki | city | Nagasaki-ken | Japan | 32.8333333 | 129.7166667 | 68 | 17274 |
| Shimosakiyama | city | Nagasaki-ken | Japan | 32.65 | 128.8833333 | 95 | 8437 |
| Shinuonome | city | Nagasaki-ken | Japan | 33 | 129.1 | 0 | 25642 |
| Shiohama | city | Nagasaki-ken | Japan | 33.3666667 | 129.8166667 | 42 | 23209 |
| Shioike | city | Nagasaki-ken | Japan | 32.85 | 128.9666667 | 0 | 13589 |
| Shiragashira | city | Nagasaki-ken | Japan | 32.6833333 | 130.1666667 | 616 | 25459 |
| Shirahama | city | Nagasaki-ken | Japan | 33.0166667 | 129.7333333 | 3 | 30320 |
| Shirato | city | Nagasaki-ken | Japan | 32.6833333 | 130.1666667 | 616 | 25459 |
| Shiroishi | city | Nagasaki-ken | Japan | 32.75 | 128.6716667 | 144 | 24323 |
| Shisa | city | Nagasaki-ken | Japan | 33.35 | 129.7166667 | 0 | 22445 |
| Shishi | city | Nagasaki-ken | Japan | 33.3058333 | 129.4397222 | 177 | 19933 |
| Shishigi | city | Nagasaki-ken | Japan | 33.2 | 129.4 | 3 | 13003 |
| Shishima | city | Nagasaki-ken | Japan | 34.5058333 | 129.3088889 | 311 | 22915 |
| Shishimi | city | Nagasaki-ken | Japan | 34.5058333 | 129.3088889 | 311 | 22915 |
| Shitaga | city | Nagasaki-ken | Japan | 34.4833333 | 129.4 | 3 | 24312 |
| Shitaka | city | Nagasaki-ken | Japan | 34.4833333 | 129.4 | 3 | 24312 |
| Shitaru | city | Nagasaki-ken | Japan | 34.5666667 | 129.3 | 3 | 20146 |
| Shitogama | city | Nagasaki-ken | Japan | 32.755 | 129 | 72 | 3656 |
| Shuji | city | Nagasaki-ken | Japan | 34.6 | 129.4333333 | 154 | 31603 |
| Shuku | city | Nagasaki-ken | Japan | 33.1333333 | 129.9 | 278 | 41030 |
| Shuku | city | Nagasaki-ken | Japan | 33.1333333 | 129.9 | 278 | 41030 |
| Shukunoura | city | Nagasaki-ken | Japan | 32.9 | 129.05 | 49 | 24144 |
| Shushi | city | Nagasaki-ken | Japan | 34.6 | 129.4333333 | 154 | 31603 |
| Shushi | city | Nagasaki-ken | Japan | 33.35 | 129.4666667 | 643 | 19546 |
| Shushimen | city | Nagasaki-ken | Japan | 33.35 | 129.4666667 | 643 | 19546 |
| Shūji | city | Nagasaki-ken | Japan | 34.6 | 129.4333333 | 154 | 31603 |
| Shūshi | city | Nagasaki-ken | Japan | 34.6 | 129.4333333 | 154 | 31603 |
| Shūshi | city | Nagasaki-ken | Japan | 33.35 | 129.4666667 | 643 | 19546 |
| Simabara | city | Nagasaki-ken | Japan | 32.7833333 | 130.3666667 | 16 | 28934 |
| Sisa | city | Nagasaki-ken | Japan | 33.35 | 129.7166667 | 0 | 22445 |
| Sisi | city | Nagasaki-ken | Japan | 33.3058333 | 129.4397222 | 177 | 19933 |
| Sisiki | city | Nagasaki-ken | Japan | 33.2 | 129.4 | 3 | 13003 |
| Sisimi | city | Nagasaki-ken | Japan | 34.5058333 | 129.3088889 | 311 | 22915 |
| So | city | Nagasaki-ken | Japan | 34.4166667 | 129.3666667 | 314 | 30224 |
| Sone | city | Nagasaki-ken | Japan | 33.0519444 | 129.0841667 | 318 | 9008 |
| Sonogi | city | Nagasaki-ken | Japan | 33.0333333 | 129.9166667 | 3 | 26013 |
| Sueishimachi | city | Nagasaki-ken | Japan | 32.6833333 | 129.8333333 | 288 | 15426 |
| Sueisi | city | Nagasaki-ken | Japan | 32.6833333 | 129.8333333 | 288 | 15426 |
| Suga | city | Nagasaki-ken | Japan | 32.85 | 130.3333333 | 16 | 21994 |
| Sugawa | city | Nagasaki-ken | Japan | 32.65 | 130.2833333 | 0 | 25059 |
| Suigetsu | city | Nagasaki-ken | Japan | 32.6166667 | 130.1666667 | 0 | 17703 |
| Suigetsutsu | city | Nagasaki-ken | Japan | 32.6166667 | 130.1666667 | 0 | 17703 |
| Sukawa | city | Nagasaki-ken | Japan | 32.65 | 130.2833333 | 0 | 25059 |
| Sumo | city | Nagasaki-ken | Japan | 34.2666667 | 129.2833333 | 301 | 30231 |
| Susaki | city | Nagasaki-ken | Japan | 32.8666667 | 129.0883333 | 328 | 9150 |
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