Objectives Irritable bowel syndrome (IBS) is associated with psychological stress, alterations in gut motor function and/or visceral perception. Previous studies suggest 7-32% of people develop I BS after bacterial gastroenteritis but the exact mechanisms underlying post-infectious IBS are not clear. The present study's aim was to examine the role of possible causative factors in the development of post-infectious functional gastro-intestinal disorders (FGIDs), including IBS. Methods A prospective cohort study where 122 people without a prior FGID under study and with stool-positive bacterial gastroenteritis consented to participate. The presence or not of IBS, functional dyspepsia or functional diarrhoea was diagnosed at the start and on 6-month follow-up using self-complete Rome 11 modular questionnaires. Demographic data, smoking, alcohol use, anxiety and depression (using the Hospital Anxiety and Depression Scale), and life events and impact (using the Life Events Survey) were collected at the start of the study. Results One hundred and seven questionnaires were returned with 25 participants (23.4%) developing a FGID and 16 participants presenting symptoms consistent with I BS (15%). Smoking was significantly associated with the development of a post-infectious FGID (odds ratio=4.8, 95% confidence interval= 1.5-15.2) on regression analysis. Conclusions Post-infectious FGIDs appear to be associated with smoking. Smoking is known to moderate gut immunity in other disorders such as ulcerative colitis and Crohn's disease. This study adds to increasing evidence for an organic basis to post-infectious FGIDs, perhaps moderated via inflammatory pathways.