The coexistence of obstructive sleep apnoea (OSA) and metabolic syndrome (MetS) substantially increase the risk of cardiovascular diseases and premature death, posing a major global health burden. Despite growing research interest, evidence on their causal relationship and underlying biological mechanisms remains relatively limited and inconsistent. This study aims to investigate the relationship between OSA and MetS using the UK Biobank (UKB) cohort. We will estimate both existing and new cases of MetS among individuals with OSA and identify risk factors associated with its development. Using bidirectional Mendelian randomisation, a genetic method for assessing cause and effect, we will explore whether OSA and MetS impose causal inferences on one another. Available data relating to proteins will also be explored to evaluate biological mediation pathways underlying metabolic dysfunction in OSA and potential drug targets for treatment. Statistical analyses will adjust for key variables such as age, sex, body weight, lifestyle, and socioeconomic factors. The integration of these data sources from the UKB will triangulate the evidence and provide a comprehensive understanding essential for more precise prevention and management of metabolic disorders related to OSA.