Usability has been identified as a key issue in health informatics. Worldwide numerous projects have been carried out in an attempt to increase and optimize health system usability. Usability testing, involving observing end users interacting with systems, has been widely applied and numerous publications have appeared describing such studies. However, to date, fewer works have been published describing methodological approaches to analyzing the rich data stream that results from usability testing. This includes analysis of video, audio and screen recordings. In this paper we describe our work in the development and application of a coding scheme for analyzing the usability of health information systems. The phases involved in such analyses are described.