In this world, I haven't visited the End or the Nether yet, so the /DIM and /DIM-1 folders have both been empty.
At some point today, after building a long rail line, I noticed that there is now a 12kb /region/r.1.1.mca in both folders, even though I haven't been to either dimension! The files are missing in my backup from yesterday, so I know they were just created.
This is a single-player map, so that precludes the possibility of another server user having visited and caused chunks to be generated.
Where did they come from? Why is Minecraft generating chunks for dimensions I haven't visited?
Best Answer
According to Notch, both Nether and The End portals spawn naturally as well. If you happen to "meet" one of these portals, it will automatically generate a single chunk in the corresponding world to be able to place the matching portal in that world.
I'm not entirely sure, even though it seems this way, that if you see one of the two, it does this for both. Notch has never released anything about this.