Phase detection is where there are pairs of sensors that are blocked left and right (or top and bottom) and from the differences, the camera has the information needed to bring the image into focus:
|IR image of the pixel array|
Chipworks first analyzed this type of technology in the Nikon V1 with an Aptina sensor MT9J007. Aptina used a set of 9 regular lines of phase AF pixels, while Canon is using a somewhat irregular pixel pattern for phase detection:
Canon patent US 2010/0165176 has a fairly detailed description of their approach.