Abstract Background Young people with complex health needs have impairments that can limit their ability to carry out day-to-day activities. As well as coping with other developmental transitions, these young people must negotiate the transfer of their clinical care from child to adult services. The process of transition may not be smooth and both health and social outcomes may suffer. Increasingly, policy-makers have recognised the need to ensure a smoother transition between children’s and adult services, with processes that are holistic, individualised, and person-centred; however, there is little outcome data to support proposed models of care. This study aims to identify the features of transitional care that are potentially effective and efficient for young people with complex health needs making their transition. Methods/Design Longitudinal cohort study. 450 young people aged 14 years to 18 years 11 months (with autism spectrum disorder and an additional mental health problem, cerebral palsy or diabetes) will be followed through their transition from child to adult services and will contribute data at baseline, 12, 24 and 36 months. We will collect data on: health and wellbeing outcomes (participation, quality of life, satisfaction with services, generic health status (EQ-5D-Y) and condition specific measure of disease control or management); exposure to proposed beneficial features of services (such as having a key worker, appropriate involvement of parents); socio-economic characteristics of the sample; use of condition-related health and personal social services; preferences for the characteristics of transitional care. We will us regression techniques to explore how outcomes vary by exposure to service features and by characteristics of the young people. These data will populate a decision-analytic model comparing the costs and benefits of potential alternative ways of organising transition services. In order to better understand mechanisms and aid interpretation, we will undertake qualitative work with 15 young people, including interviews, non-participant observation and diary collection. Discussion This study will evaluate the effect of service components of transitional care, rather than evaluation of specific models that may be unsustainable or not generalisable. It has been developed in response to numerous national and international calls for such evaluation.