Abstract Background The umbrella term Variations of Sex characteristics (VSCs), also known as Intersex variations, indicates the lived experience of the socio-cultural consequences of being born with a body that does not fit the normative social constructions of male and female (Van der Have, 2016). Currently, there is not a universal consensus on the ‘management' of VSCs, and the existing guidelines and recommendation vary depending on the chosen disciplinary perspective. However, normalising interventions are still guided by sociocultural reasons. Methods Starting from a qualitative research involving 65 semi-structured interviews with health professionals and ethnographic observations in 2 hospitals and 2 patients' associations conducted in Italy between 2015 and 2017, this presentation explores how beliefs systems play a crucial role in maintaining the medical status quo through cultural and gender biases. Results Whether it be sexual health, psychological wellbeing, physical features, other syndromes, transgender identity or sexual orientation, participants' beliefs frequently drifted to cultural rather than clinical interpretations of VSC. Results show that health professionals' experience of VSC include (1) social, (2) medical and (2) gender biases as guiding principle in the assessment of intersex variations, denoting cultural concepts of ‘abnormal' behaviours, identities, sexual orientation and gender roles as VSCs' frames of meaning. Conclusions Despite the increasing international awareness around intersex human rights, results show the critical role of belief systems in maintaining VSC's surgical and social erasing processes, reinforcing the need to consider the mediating aspects - culture, religion and social factors - that affect different social contexts when assessing intersex human rights, social policies and professional training.