A method and apparatus for aligning a scan pattern to a two dimensional bar code having parallel rows of codewords. The two dimensional bar code is scanned with a scanning pattern oriented such that a plurality of lines thereof cross the bar code rows. A determination if there is a non-zero angle between at least one of the plurality of lines and the rows by decoding codewords in rows intersected by the at least one line is made and the orientation of the scanning pattern is adjusted to reduce the absolute value of the angle.