Which directories does the Media Scanner scan? Which directories does the Media Scanner scan at startup?

Is it only the sdcard?
Media Scanner scans both SD card as well as USB storage, but not ROM and system storage. Means, it scans from /sdcard/ and /sdcard/external_sd/ mount points. It goes deep inside all non-hidden sub-directories, unless .nomedia file is detected.

Media Scanner skips ROM and system storage because both require root permission to write anything there. And, its very unlikely for an end-user to store music, photo there.