The question of what temperament, exactly, Bach meant by "Well-Tempered" is a hotly contested question, with the majority assuming it is one of the Werkmeister variants, and a vocal minority insisting it was Bach's own custom temperament, with a couple of Bach scholars even hypothesizing that Bach encoded his temperament scheme into the decorative squiggle on the cover page of the original printing of the book.

But everyone agrees it wasn't equal temperament. The point of the book was to showcase the unique character of each key, uniqueness that is lost in equal temperament.