Purpose: The purpose of this paper is to discuss heuristic evaluation as a method for evaluating e-learning courses and applications and more specifically to investigate the applicability and empirical use of two customized e-learning heuristic protocols. Design/methodology/approach: Two representative e-learning heuristic protocols were chosen for the comparative analysis. These protocols augment the "traditional" heuristic sets so as to cover technology-enhanced learning properties. Two reviewers that have considerable experience in usability evaluation as well as in e-learning were involved in this comparative analysis. Coverage, distribution and redundancy were employed as three basic criteria for conducting the evaluation. Findings: The main results of the study indicate that both heuristic protocols exhibit wide coverage of potential usability problems. The distribution of usability problems is uneven to a large number of heuristics for both heuristic sets, which reveals that some heuristics are more general than others. Originality/value: This study shows the empirical application of two heuristic protocols in a usability evaluation of e-learning applications. Furthermore, it provides a comparison of the two heuristic sets according to a set of criteria and provides a first set of suggestions regarding further development and validation of these heuristic sets. (Contains 5 tables.)