Background: Many large studies have complex advisory committee structures, yet there is no empirical evidence regarding their optimal composition, scope and contribution. The aim of this study was to inform the committee and advice infrastructure for future research studies. Methods: In the context of a five-year study funded by the UK National Institute for Health Research, three advisory committees were formed. In addition, advice was obtained from individual experts. All recommendations received in the start-up phase (first seven months) of the study were recorded, along with the decision about implementation of the recommendation. A particular focus was on the impact of public involvement. Results: A total of 172 recommendations were made, including 70 from 20 individual experts. The recommendations were grouped into five emergent themes: Scientific, Pragmatic, Resources, Committee and Collaboration. Most recommendations related to strengthening existing components or adding new components to the study protocol. Very few recommendations either proposed removing study components or contradicted other recommendations. Three 'implementation criteria' were identified: scientific value, pragmatic feasibility, and paradigmatic consistency. 103 (60%) of recommendations were implemented and 25 (15%) were not implemented. The benefits identified by the research team were improved quality and confidence, and the costs were increased cognitive demands, protocol revision time, and slower progress. Conclusions: The findings are discussed in the context of the wider literature on public involvement in research. Six recommendations are identified. First, have a clear rationale for each advisory committee expressed as terms of reference, and consider the best balance between committees and individual consultation with experts. Second, an early concern of committees is inter-committee communication, so consider cross-representation and copying minutes between committees. Third, match the scope of advisory committees to the study, with a less complex advisory structure for studies with more finalised designs. Fourth, public involvement has a mixed impact, and relies on relationships of trust, which take time to develop. Fifth, carefully consider the match between the scientific paradigm applied in the study and the contribution of different types of knowledge and expertise, and how this will impact on possibilities for taking on advice. Finally, responding to recommendations uses up research team resources, and the costs can be reduced by using the three implementation criteria.