Each keyboard of the organ (manual or pedal) usually controls a separate division of the instrument with its own pipes and stops. There is no standard number of stops in these divisions, so one can't tell how large an instrument is simply by the number of keyboards it has. The nice thing about having more than two manual keyboards is that tone color changes may be made simply by moving the hands to another manual instead of by changing stops.

Stops may be played on another keyboard than their own by means of couplers. On a large electric action instrument, these couplers (usually found on tablets above the top manual) are available at different pitch levels - 16', 8', and 4', which means that all of the stops can be coupled at their normal pitch, or an octave lower, or an octave higher. On many organs one can also couple a manual to itself an octave higher or an octave lower.

The Great (Hauptwerk, Grand Orgue) is the main division of the organ. It is generally the lower manual on two-manual instruments and the middle manual on three-manual organs. The other manuals can usually be coupled to the Great, so the loudest sounds are played on it. The Great can also be coupled to the Pedal. It will nearly always contain some sort of principal chorus - principals at 8', 4', possibly 2 2/3', 2', and one or more mixtures. A large organ may have a 16' principal chorus on the Great - principals at 16', 8', maybe 5 1/3', 4', 2', a low mixture and a high one. Instead, there may be a 16' stop on the Great such as a Bourdon or Quintadena to add to the 8' chorus. There will usually be flute stops on the Great - a rather wide-scale 8' flute and possibly 4' and 2' flutes as well. On two-manual instruments one will often find mutations and solo reeds on the Great also. If there is a string, it will usually be a big 8' Gamba. If there is one reed, it will often be an 8' Trumpet. On large instruments there might be chorus reeds at 16', 8', and 4'.