Working outside of regular daytime hours is increasingly common in current societies and poses a substantial challenge to an individual’s biological rhythm. Disruptions of the gastrointestinal tract’s circadian rhythm and poor dietary choices subsequent to shiftwork may predispose the shift workforce to an increased risk of gastrointestinal disorders, including constipation, peptic ulcer disease, and erosive gastritis. We investigated bowel health in a US population of shift workers, using data from the National Health and Nutrition Examination Survey, and compared bowel movement (BM) frequency and defecation patterns between 2007 day workers and 458 shift workers (representing 55,305,037 US workers). Using bivariate and multivariate logistic regression techniques, our results suggested no association between shiftwork status and BM frequency, bowel leakage of gas, and stool consistency. Constipation prevalence was high but comparable in both groups (6.90% vs. 7.09%). The low fiber intake observed in both groups (15.07 vs. 16.75 g/day) could play a potential role here. The two groups did not differ with regard to other nutrients that may influence BM frequency and stool consistency (e.g., carbohydrate or caffeine intake). Additional studies including food group analyses and fecal biomarkers are warranted for a better understanding of GI health in shift workers.