Background: Cardiovascular disease has a multifactorial aetiology with a number of both modifiable and non-modifiable risk factors. Although evidence indicates that dietary intake plays an important role, few studies have focused on the effect of fruit and vegetable consumption on early markers of vascular function. Therefore, we hypothesised that supplementation with capsules containing a combination of fruit and vegetable extracts over 12 weeks can significantly modulate biomarkers of vascular function compared with a control group receiving placebo. Methods/Design: This is a double-blind, randomised controlled trial that includes overweight and obese but otherwise healthy participants. Participants are randomly allocated to one of two groups: active supplementation (encapsulated fruit and vegetable powder) or placebo taken twice daily for 12 weeks, whereas both groups will be given the '5-A-Day' dietary advice. The primary outcome is to measure changes to the carotid intima media thickness (cIMT) between the two groups from baseline (test visit 1) to 12 weeks later (test visit 2). The secondary outcomes include macro- and microvascular changes and changes to blood markers. Discussion: In addition to the primary and secondary objectives, this explanatory trial incorporates potential novel biomarkers such as trimethylamine-N-oxide (TMAO) and lipopolysaccharide (LPS). Trial registration:ISRCTN14315618. Registration date 27 February 2014.