The invention relates to a method of estimating the alignment in the printing medium direction between a first and a second pen of a printing system having a scan axis, whereby: the first, respectively second pen prints a first, respectively second pattern element; the first and second pattern elements are substantially aligned and separated by a space along the scan axis; each of the first and second pattern elements comprises a first and an associated second mark separated by a blank along the scan axis, the first and the second marks being staggered in the printing medium direction; an optical sensor scans along the scan axis over the first and second pattern elements, an analysis of the sensor output leading to estimating the alignment.