Physicians' empathy is generally regarded as important and attempts are made to foster empathy. However, research indicates that the medical students' empathy is often stunted during medical education, and our understanding of how empathy is modulated during medical education is limited. This critical review explores some relatively-neglected challenges in the literature on empathy development in medical education. There is a lack of adequate attention to physicians' disciplinary matrix, the medico-scientific formation of physicians is often neglected, the dichotomy between the science and the humanities lives on and the 'soft' side is often presented as an appendix. This may contribute to sustain a double-blinded, dichotomized clinical gaze--a clinical gaze that tends to separate biomedical aspects from human experience and understanding and to neglect existential aspects of both the physician and the patient. Empathy training and the humanities should not be situated outside the hard core of medicine, but rather foster critical discussions of the limits and strengths of biomedical paradigms throughout medicine. In this way, the gap between biomedicine and the humanities could be bridged, and empathy training could contribute both in developing physicians' general clinical perception and judgement and in preventing the widespread stunting of empathy.