A method for automatic pen alignment in a printing apparatus, wherein the printing apparatus has a scan direction or x-axis and a media advance direction or y-axis, orthogonal to said scan direction or x-axis, the method comprising the steps of performing a pen alignment process, determining an alignment correction algorithm to be applied during subsequent printing, to compensate for the misalignment determined in said pen alignment process, measuring an output angle of the media, defined as the angle between the y-axis and the actual direction of advance of the media, with at least one optical sensor arranged stationary on the printing apparatus, and employing the measured output angle to modify the alignment correction algorithm to be applied during subsequent printing.