Before Bach's tempered scale (what we use now), my understanding is that perfect 3rds and perfect 5ths were used which made music sound different than it does now, and it also made only a few keys practical for performance: all naturals and probably up to 1 or 2 sharps or flats (C, G, D, F, Bb). With these 5 keys, all 12 notes are known and used, but at first tuned differently from now.
*COUGH BACH NEVER USED EQUAL TEMPERAMENT COUGH*