Introduction: Contextual factors (eg, diagnostic suggestion and burnout) can affect physician clinical reasoning performance, leading to diagnostic error. Yet, contextual factors have only recently been studied and none of that work focused on how physicians appraise (ie, evaluate) the clinical situation as they reason. The purpose of this qualitative study was to use appraisal to describe the effect of contextual factors on clinical reasoning. Materials and Methods: Physicians (n = 25) either viewed two video cases or participated in two live scenarios, one with contextual factors and one without. Afterwards, they completed a "think-aloud" reflection while reviewing the cases. Transcribed think-alouds were coded for appraisal markers, comparing cases with and without contextual factors. Results: When contextual factors were present, participants expressed more emotional evaluation and uncertainty about those emotions. Across all types of cases, participants expressed uncertainty about the case and assessed what "could" or "would" have gone differently. Conclusions: This study suggests that one major effect of contextual factors may be that they induce emotions, which may affect the process of clinical reasoning and diagnostic error. It also suggests that uncertainty may be common in clinical practice, and we should thus further explore its impact.