New surgical technologies may challenge societal values, and their adoption may lead to ethical challenges. Despite proven cost-effectiveness, obesity (bariatric) surgery and its public funding have been questioned on ethical arguments relating to, for example, the self-inflicted or non-disease nature of obesity. Our aim was to analyze the ethical issues relevant to bariatric surgery. A comprehensive health technology assessment was conducted on bariatric surgery for morbid obesity using the EUnetHTA method, including a fully integrated ethical analysis. The ethical arguments suggesting that obesity should not be surgically treated because it is self-inflicted were rejected. Medicalization of obesity may have both positive and negative effects that impact the various stakeholders differently, thus being difficult to balance. Informing bariatric surgery patients and actively supporting their autonomy is exceptionally important, as the benefits and harms of both obesity and bariatric surgery are complex, and the outcome depends on how well the patient understands and adheres to the life-long changes in eating habits required. Justice considerations are important in organizing surgical treatment of obesity, as the obese are discriminated against in many ways and obesity is more common in socioeconomically disadvantaged populations who might have problems of access to treatments. Obesity should be treated like other diseases in health care, and obesity surgery rationed like other cost-effective treatments. Positive actions to ensure patient autonomy and just access to surgical treatments may be warranted.