Objectives Peristalsis can lead to confusing FDG PET bowel uptake artefacts and potential for recording inaccurate mean standardised uptake value (SUV) measurements in PET-CT scans. Accordingly, we investigate the influence of different SUV normalisations on FDG PET uptake of the bowel and assess which one(s) have least dependence on body size factors in patients with and without the introduction of the anti-peristalsis agent N-butylscopolamine (Buscopan). Methods This study consisted of 92 prospective oncology patients, each having a whole body 18F-FDG PET scan. Correlations were investigated between height, weight, glucose, body mass index (bmi), lean body mass (lbm) and body surface area (bsa) with maximum and mean SUV recorded for bowel normalised to weight (SUVw), lbm (SUVlbm), bsa (SUVbsa) and blood glucose corrected versions (SUVwg, SUVlbmg, SUVbsag). Results Standardised uptake value normalisations were significantly different between control and Buscopan groups with less variability experienced within individual SUV normalisations by the administration of Buscopan. Mean SUV normalisations accounted for 80% of correlations in the control group and 100% in the Buscopan group. Further, >86% of all correlations across both groups were dominated by mean SUV normalisations of which, about 69% were accounted for by SUVbsa and SUVbsag. Conclusions We recommend avoiding mean SUVbsa and individual glucose normalisations especially, mean SUVbsag as these dominated albeit relatively weak correlations with body size factors in control and Buscopan groups. Mean and maximum SUVw and SUVlbm were shown to be independent of any body size parameters investigated in both groups and therefore considered suitable for monitoring FDG PET uptake in the normal bowel for our patient cohort.