In sports medicine and rehabilitation of musculoskeletal conditions, training, knowledge and expertise of clinicians are the guarantors of good clinical practice. But are they really? Since the 1970s, a growing body of sociological and behavioral science has developed the concepts of cognitive biases and thinking errors. In a nutshell, it tries to explain how we approach decision-making using shortcuts, or heuristics. Our brains will alternatively use 2 systems to think and decide: system 1 is fast, intuitive and emotional, whereas system 2 is slow, logical and conscious. We may think clinicians use the latter systematically, but they actually use system 1 in many situations. Whether due to intrinsic thinking errors or external forces that cloud our judgment, we are under unconscious influences and so are all the stakeholders in the rehabilitation setting, including the patient/athlete. We present some of the most prevalent biases that pervade clinical decision-making and attempt to give a bit of background context starting from the typical tension between academic authority and personal experience. The field of sports performance is also riddled with beliefs, egocentrism and a general tendency to search for magic bullets that will bring the marginal gains and edge over the competition. This plays into the rehabilitation of patient-athletes in different ways. Finally, there are ways to mitigate the effect of cognitive biases to improve decision-making. This must include better communication, shared decisions and ultimately the understanding that we should drive our profession to deliver high-value care tailored to the patients, in line with the best evidence at the best possible cost. Hopefully, we can shed some light without too many of our own biases on the complexities of thinking in sports medicine and rehabilitation.