23 cities
| City | Rank | 2026 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| La Crescent | 1 | 5,214 | 5,342 | -0.4% | 1,550 | 3 | City |
| Caledonia | 2 | 2,718 | 2,864 | -0.88% | 962 | 3 | City |
| Spring Grove | 3 | 1,175 | 1,255 | -1.09% | 1,182 | 1 | City |
| La Crescent | 4 | 1,011 | 1,054 | -1.08% | 50 | 20 | Township |
| Houston | 5 | 955 | 999 | -0.73% | 776 | 1 | City |
| Caledonia | 6 | 596 | 624 | -1.16% | 18 | 34 | Township |
| Money Creek | 7 | 552 | 578 | -1.25% | 16 | 36 | Township |
| Mound Prairie | 8 | 547 | 570 | -1.08% | 15 | 36 | Township |
| Brownsville | 9 | 534 | 567 | -0.93% | 289 | 2 | City |
| Hokah | 10 | 525 | 554 | -0.94% | 751 | 1 | City |
| Hokah | 11 | 419 | 444 | -1.64% | 18 | 23 | Township |
| Wilmington | 12 | 407 | 428 | -1.45% | 11 | 36 | Township |
| Brownsville | 13 | 389 | 411 | -1.52% | 14 | 28 | Township |
| Houston | 14 | 382 | 399 | -1.04% | 12 | 33 | Township |
| Mayville | 15 | 344 | 357 | -0.86% | 11 | 31 | Township |
| Spring Grove | 16 | 322 | 341 | -1.53% | 9 | 35 | Township |
| Yucatan | 17 | 311 | 330 | -1.58% | 7 | 43 | Township |
| Union | 18 | 305 | 323 | -1.61% | 12 | 26 | Township |
| Sheldon | 19 | 278 | 295 | -1.77% | 9 | 30 | Township |
| Black Hammer | 20 | 258 | 273 | -1.53% | 7 | 36 | Township |
| Eitzen | 21 | 258 | 270 | -0.77% | 423 | 1 | City |
| Crooked Creek | 22 | 241 | 252 | -1.23% | 8 | 31 | Township |
| Jefferson | 23 | 125 | 132 | -1.57% | 4 | 29 | Township |
La Crescent is the largest city in Houston County, with a population of 5,214.
Jefferson is the smallest city in Houston County, with a population of 125.
There are 23 cities in Houston County, Minnesota.