In system design, many diagrams of many different types are used. Diagrams communicate design aspects between members of the development team, and between these experts and the non-expert customers and future users. Mastering the creation of diagrams is often a challenging task, judging by particular errors persistently found in diagrams created by undergraduate computer science students. We assume a possible misalignment between human perception and cognition on the one hand and the diagrams’ structure and syntax on the other. This article presents the results of an investigation of such a misalignment. We focus on the deployment of so-called 'conceptual user models' (mental models, created by users in their mind) at the creation of diagrams. We propose a taxonomy for mental mappings, used for categorization of representations. We describe an experiment where naive and novice subjects created one or several diagrams of a familiar task. We use our taxonomy for analysing these diagrams, both for the represented task structure and the symbols used. The results indeed show a mismatch between mental models and currently used diagram techniques