Abstract Background New guidelines in the Consensus Statement on Management of Intersex Disorders by the Lawson Wilkins Pediatric Endocrine Society/European Society for Paediatric Endocrinology Consensus Group 2006 introduced multidisciplinary teams (MDTs) to provide care that involves collaboration between healthcare professionals, parents, and children with variations of sex characteristics (VSC). Aim The aim of this study was to examine a neglected but important field of collaboration among healthcare professionals and peer support groups who provide care for people with VSC. Outcomes The study outcome was the information obtained regarding the actual composition and collaboration of the multidisciplinary teams caring for children with VSC, including their collaboration with parents, peer support groups, and other care providers. Methods In this study we used an exploratory qualitative design based on mixed focus groups (in terms of professional background) and reflexive thematic analysis. Semi-structured focus group interview guides were used to obtain information about the participants’ viewpoints on the composition and challenges of, and collaboration between, peer support groups and members of multidisciplinary teams working to care for children with VSC and their parents. Seven focus groups were conducted with healthcare professionals and peer support groups in care teams in Central, Northern, and Western Europe. The data from the focus groups were examined using reflexive thematic analysis. Results The participants in the focus groups provided information regarding the use of multidisciplinary and interdisciplinary child- and family-oriented approaches and the strengths and challenges of collaboration and peer support groups. The results showed that the teams used a predominantly multidisciplinary approach and suffered from a lack of psychosocial providers, poor collaboration with peer support groups, and poor implementation of shared decision-making to address the clinical uncertainty of parents and people with VSC. Clinical Implications Clinicians should provide more psychosocial support and improve collaboration with peer support groups and nonmedical professionals. Strengths and Limitations This study is one of the first qualitative studies to provide information on the collaboration of multidisciplinary teams working to provide care for children with VSC and collaborate with their parents in the European context. However, due to language barriers, the dropout rate of participants, and the under-representation of peer support groups in the sample there was a lack of information on collaboration among healthcare professionals and peer support groups. Conclusions The collaboration between MDTs and parents does not involve adequate psychosocial and peer support or shared decision-making to address the uncertainty experienced by children and families when faced with information about variations of sex characteristics.