<p>The perception held by clinical teachers of health professionals that their teaching efforts are under-valued by their education institutions persists despite intensive research and subsequent interventions to address this global problem. The purpose of this multi-site study is to examine how clinical teaching activities are organised, in order to reveal if there are underlying systemic factors that may contribute to this wicked problem. This study employed a cross-comparative case study design of one Singaporean and one Canadian medical school. Semi-structured interviews were conducted with organisational leaders (n = 23) who manage clinical teaching activities and/or have insights on their local assessment, support and recognition systems. Public records were also collected from each site (n = 24). A theory-driven content analysis using a complexity science interpretation of the concept of the Hidden Curriculum was conducted with both sets of data. The two sites were at different stages of maturation in respect of clinical teaching evaluation and feedback, support, and recognition and reward systems. Despite this, the interviews identified shared structure, process and culture-oriented challenges: low prioritisation of teaching, faculty demotivation and dissatisfaction across both research sites. Our findings suggest that a continued focus on structure and process-oriented reforms to elicit change is insufficient. Instead, further examination of site-specific, multiple intersecting academic and clinical cultures is needed. Future efforts to improve the value and drive the pursuit of teaching excellence will require multi-faceted structure, process and culture change approaches. We argue that Hafferty and Castellani’s (The hidden curriculum: A theory of medical education, Routledge, 2009) re-conceptualisation of hidden curriculum through a complexity science lens should be used as a heuristic device to address future research and reform in local medical education contexts.</p>