| Name | What | Region | Country | Lat | Long | Elev Ft. | Pop Est |
| Yaakna | city | Laanemaa | Estonia | 58.9813889 | 23.9955556 | 144 | 1065 |
| Yadivere | city | Raplamaa | Estonia | 58.685 | 24.4530556 | 88 | 1259 |
| Yagala | city | Harjumaa | Estonia | 59.4172222 | 25.2386111 | 164 | 9732 |
| Yago | city | Vorumaa | Estonia | 57.85 | 26.6833333 | 262 | 1559 |
| Yagu | city | Vorumaa | Estonia | 57.85 | 26.6833333 | 262 | 1559 |
| Yakobi | city | Parnumaa | Estonia | 58.6058333 | 24.5152778 | 68 | 1523 |
| Yakobi | city | Vorumaa | Estonia | 57.7 | 26.6833333 | 219 | 1568 |
| Yaksi | city | Tartumaa | Estonia | 58.5269444 | 26.6441667 | 187 | 3180 |
| Yalalype | city | Jarvamaa | Estonia | 59.0547222 | 25.8536111 | 318 | 1303 |
| Yalase | city | Raplamaa | Estonia | 58.9705556 | 24.6233333 | 200 | 1050 |
| Yalevere | city | Viljandimaa | Estonia | 58.6013889 | 25.4138889 | 170 | 1508 |
| Yalgimyae | city | Harjumaa | Estonia | 59.3191667 | 24.6016667 | 147 | 9804 |
| Yalukse | city | Laanemaa | Estonia | 59.0269444 | 23.7780556 | 111 | 1064 |
| Yaluse | city | Raplamaa | Estonia | 59.1202778 | 24.9622222 | 272 | 2474 |
| Yama | city | Ida-Virumaa | Estonia | 59.0416667 | 27.7119444 | 91 | 3960 |
| Yamaya | city | Saaremaa | Estonia | 58.052778 | 22.0566667 | 0 | 404 |
| Yamma | city | Saaremaa | Estonia | 58.052778 | 22.0566667 | 0 | 404 |
| Yan'd'ya | city | Jarvamaa | Estonia | 58.7458333 | 25.3255556 | 216 | 1343 |
| Yanamyyza | city | Hiiumaa | Estonia | 58.7483333 | 22.5113889 | 13 | 592 |
| Yaneda | city | Jarvamaa | Estonia | 59.2458333 | 25.7044444 | 255 | 2257 |
| Yanika | city | Harjumaa | Estonia | 59.1519444 | 24.3222222 | 183 | 9850 |
| Yanistvere | city | Parnumaa | Estonia | 58.5494444 | 24.1352778 | 75 | 1526 |
| Yannima | city | Harjumaa | Estonia | 59.1833333 | 24.0666667 | 144 | 9429 |
| Yanʼdʼya | city | Jarvamaa | Estonia | 58.7458333 | 25.3255556 | 216 | 1343 |
| Yaravere | city | Viljandimaa | Estonia | 58.4208333 | 25.3969444 | 252 | 1607 |
| Yaravere | city | Jarvamaa | Estonia | 58.7472222 | 25.7697222 | 239 | 1330 |
| Yarise | city | Saaremaa | Estonia | 58.5027778 | 22.445 | 118 | 1074 |
| Yarizi | city | Laanemaa | Estonia | 58.6658333 | 23.6819444 | 52 | 1078 |
| Yarni | city | Laane-Virumaa | Estonia | 59.2836111 | 26.2694444 | 393 | 1660 |
| Yarsi | city | Harjumaa | Estonia | 59.3708333 | 25.0294444 | 187 | 9791 |
| Yarumetsa | city | Parnumaa | Estonia | 58.4002778 | 23.9363889 | 49 | 1531 |
| Yarva-Madise | city | Jarvamaa | Estonia | 59.1163889 | 25.6586111 | 291 | 1302 |
| Yarva-Yani | city | Jarvamaa | Estonia | 59.0386111 | 25.8863889 | 334 | 1316 |
| Yarvakandi | city | Raplamaa | Estonia | 58.8688889 | 24.7519444 | 177 | 1051 |
| Yarvakandi | city | Raplamaa | Estonia | 58.9 | 24.8333333 | 232 | 1050 |
| Yarvayye | city | Laane-Virumaa | Estonia | 59.1958333 | 26.1566667 | 419 | 1666 |
| Yarve | city | Saaremaa | Estonia | 58.1886111 | 22.2683333 | 0 | 652 |
| Yarve | city | Parnumaa | Estonia | 58.6166667 | 24.1597222 | 78 | 1523 |
| Yarve | city | Harjumaa | Estonia | 59.4166667 | 24.6330556 | 72 | 6176 |
| Yarve | city | Parnumaa | Estonia | 58.6902778 | 24.7133333 | 127 | 1481 |
| Yarve | city | Viljandimaa | Estonia | 58.1769444 | 25.9705556 | 187 | 1304 |
| Yarve | city | Tartumaa | Estonia | 58.3183333 | 26.3077778 | 262 | 4085 |
| Yarve | city | Ida-Virumaa | Estonia | 59.4058333 | 27.3111111 | 239 | 4381 |
| Yarve-Keskranna | city | Saaremaa | Estonia | 58.2008333 | 22.2975 | 0 | 387 |
| Yarvekyula | city | Saaremaa | Estonia | 58.5730556 | 22.8402778 | 42 | 1073 |
| Yarvekyulya | city | Harjumaa | Estonia | 59.4166667 | 24.6330556 | 72 | 6176 |
| Yarvekyulya | city | Harjumaa | Estonia | 59.3766667 | 24.7927778 | 154 | 9475 |
| Yaska | city | Viljandimaa | Estonia | 58.5411111 | 25.5897222 | 203 | 1601 |
| Yatma | city | Laane-Virumaa | Estonia | 59.4261111 | 26.5091667 | 206 | 1653 |
| Yauni | city | Saaremaa | Estonia | 58.4383333 | 22.2277778 | 108 | 1062 |
| Yauza | city | Hiiumaa | Estonia | 58.7777778 | 22.7033333 | 26 | 658 |
| Yayetma | city | Laane-Virumaa | Estonia | 58.9166667 | 26.4166667 | 328 | 1659 |
| Yelbu | city | Parnumaa | Estonia | 58.5133333 | 24.5272222 | 49 | 1526 |
| Yepa | city | Parnumaa | Estonia | 58.5666667 | 24.2333333 | 78 | 1526 |
| Yerma | city | Hiiumaa | Estonia | 58.8005556 | 22.4758333 | 39 | 625 |
| Yermakozu | city | Harjumaa | Estonia | 59.3961111 | 25.47 | 265 | 9777 |
| Yeste | city | Saaremaa | Estonia | 58.5416667 | 22.7372222 | 42 | 835 |
| Yeypri | city | Laane-Virumaa | Estonia | 59.1308333 | 26.3344444 | 410 | 1667 |
| Yeyre | city | Raplamaa | Estonia | 58.8683333 | 24.91 | 226 | 1051 |
| Yinigu | city | Hiiumaa | Estonia | 58.8505556 | 22.4663889 | 49 | 755 |
| Yinnigu | city | Hiiumaa | Estonia | 58.8505556 | 22.4663889 | 49 | 755 |
| Ykha | city | Saaremaa | Estonia | 58.3994444 | 22.5397222 | 49 | 1097 |
| Yle | city | Jarvamaa | Estonia | 58.9833333 | 25.8333333 | 291 | 1303 |
| Yogeva | city | Jogevamaa | Estonia | 58.7466667 | 26.3938889 | 229 | 1264 |
| Yokhvi | city | Ida-Virumaa | Estonia | 59.3591667 | 27.4211111 | 183 | 4680 |
| Yudruma | city | Laanemaa | Estonia | 58.8116667 | 24.0755556 | 42 | 1069 |
| Yukhasel'ya | city | Parnumaa | Estonia | 58.3691667 | 24.6425 | 45 | 1531 |
| Yukhaselʼya | city | Parnumaa | Estonia | 58.3691667 | 24.6425 | 45 | 1531 |
| Yuksnurme | city | Harjumaa | Estonia | 59.2919444 | 24.6111111 | 134 | 9804 |
| Yul'de | city | Viljandimaa | Estonia | 58.5227778 | 25.6605556 | 203 | 1601 |
| Yula | city | Raplamaa | Estonia | 58.9841667 | 24.8136111 | 242 | 1050 |
| Yuleval'tkyula | city | Harjumaa | Estonia | 59.3833333 | 24.4 | 101 | 9555 |
| Yulevalʼtkyula | city | Harjumaa | Estonia | 59.3833333 | 24.4 | 101 | 9555 |
| Yuleyye | city | Raplamaa | Estonia | 59.041667 | 24.8469444 | 249 | 1047 |
| Yuleyye | city | Harjumaa | Estonia | 59.3413889 | 25.3697222 | 196 | 9791 |
| Yulgase | city | Harjumaa | Estonia | 59.4866667 | 25.0777778 | 177 | 7054 |
| Yulʼde | city | Viljandimaa | Estonia | 58.5227778 | 25.6605556 | 203 | 1601 |
| Yuminda | city | Harjumaa | Estonia | 59.6283333 | 25.5202778 | 3 | 2086 |
| Yuna | city | Jogevamaa | Estonia | 58.7433333 | 26.355 | 265 | 1264 |
| Yunnaste | city | Parnumaa | Estonia | 58.5991667 | 24.9066667 | 88 | 1522 |
| Yur'yev | city | Tartumaa | Estonia | 58.3661111 | 26.7361111 | 118 | 4081 |
| Yurev | city | Tartumaa | Estonia | 58.3661111 | 26.7361111 | 118 | 4081 |
| Yuri | city | Harjumaa | Estonia | 59.3541667 | 24.8941667 | 200 | 9791 |
| Yuriksma | city | Parnumaa | Estonia | 58.6166667 | 24.6666667 | 78 | 1523 |
| Yursi | city | Saaremaa | Estonia | 58.3933333 | 22.8383333 | 36 | 1088 |
| Yuru | city | Raplamaa | Estonia | 59.0647222 | 24.9502778 | 282 | 1047 |
| Yuru-Saunakyula | city | Raplamaa | Estonia | 59.05 | 24.9333333 | 282 | 1047 |
| Yurʼyev | city | Tartumaa | Estonia | 58.3661111 | 26.7361111 | 118 | 4081 |
| Yusse | city | Laanemaa | Estonia | 58.93 | 23.6891667 | 39 | 1023 |
| Yutapere | city | Raplamaa | Estonia | 59.0847222 | 24.4052778 | 187 | 7187 |
| Yvi Pervyye | city | Tartumaa | Estonia | 58.4647222 | 26.5436111 | 144 | 3713 |
| Yvi Vtoroye | city | Tartumaa | Estonia | 58.4833333 | 26.55 | 164 | 3713 |
| Yyarva-Yani | city | Jarvamaa | Estonia | 59.0386111 | 25.8863889 | 334 | 1316 |
| Yyeere | city | Laanemaa | Estonia | 58.7758333 | 24.0938889 | 36 | 1066 |
| Yyeertse | city | Parnumaa | Estonia | 58.6833333 | 25.1166667 | 147 | 1436 |
| Yyeeru | city | Raplamaa | Estonia | 58.815 | 24.4208333 | 104 | 1054 |
| Yyekyula | city | Parnumaa | Estonia | 58.5333333 | 24.6166667 | 52 | 1526 |
| Yyekyula | city | Raplamaa | Estonia | 58.7908333 | 25.1241667 | 190 | 1106 |
| Yyesu | city | Harjumaa | Estonia | 59.4677778 | 25.1644444 | 111 | 6836 |
| Yyesu | city | Viljandimaa | Estonia | 58.3827778 | 26.1361111 | 154 | 2063 |
| Yygeva | city | Jogevamaa | Estonia | 58.7466667 | 26.3938889 | 229 | 1264 |
| Yygisu | city | Harjumaa | Estonia | 59.2783333 | 24.5105556 | 137 | 9815 |
| Yykhvi | city | Ida-Virumaa | Estonia | 59.3591667 | 27.4211111 | 183 | 4680 |
| Yysu | city | Viljandimaa | Estonia | 58.1972222 | 25.5502778 | 305 | 1615 |
| Yyuga | city | Ida-Virumaa | Estonia | 59.1441667 | 27.3602778 | 170 | 4708 |
| Yyyepera | city | Tartumaa | Estonia | 58.2633333 | 27.4358333 | 55 | 2257 |
| Yyyezu | city | Viljandimaa | Estonia | 58.3827778 | 26.1361111 | 154 | 2063 |
| Yyysmyae | city | Harjumaa | Estonia | 59.4202778 | 24.6411111 | 72 | 6176 |
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