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Gastric bypass surgery leads to significant and sustained weight loss and a reduction in associated health risks in individuals with severe obesity. While reduced energy intake (EI) is the primary driver of weight loss following surgery, the underlying mechanisms accounting for this energy deficit are not well understood. The evidence base has been constrained by a lack of fit-for-purpose methodology in assessing food intake coupled with follow-up studies that are relatively short-term. This paper describes the underlying rationale and protocol for an observational, fully residential study using covert, objective methodology to evaluate changes in 24-hr food intake in patients (n = 31) at 1-month pre-surgery and 3-, 12- and 24-months post-surgery, compared to weight-stable controls (n = 32). The main study endpoints included change in EI, macronutrient intake, food preferences, and eating behaviours (speed, frequency, and duration of eating). Other physiological changes that may influence EI and weight regulation including changes in body composition, circulating appetite hormones, resting metabolic rate, total energy expenditure and gastrointestinal symptoms were also evaluated. Understanding which mechanisms contribute to a reduction in EI and weight loss post-surgery could potentially help to identify those individuals who are most likely to benefit from gastric bypass surgery as well as those that may need more targeted intervention to optimise their weight loss post-surgery. Furthermore, clarification of these mechanisms may also inform targeted approaches for non-surgical treatments of obesity.