Gastrointestinal functional disorders are characterized by abnormalities in motility with visceral hypersensitivity, representing a global public health problem. We aimed to determine whether eating habits, lifestyle characteristics, and body mass index (BMI) are associated with gastrointestinal health risk. The Gastrointestinal Health (GIH) test of the World Gastroenterology Organization (WGO) and the Roma IV criteria were applied. We obtained information on food consumption habits and aerobic exercise, among other variables. Not exercising regularly, drinking water and eating vegetables less than recommended, having high body weight, and taking symptomatic medication were variables that explained 73% of the probabilities of not having good GIH (R2 = 0.734). According to Rome IV criteria, women had a 50% higher risk than men of having functional bowel disorder (RR 1.6, 95% CI: 1.04, 2.45). Among the men studied, eating few or no vegetables and drinking less than 1 L of water daily was more frequent; however, the women had significantly more intestinal symptoms. In addition, constipation was higher among women than men (p = 0.020). All of the above explains the prognostic value of eating habits and the importance of paying attention to body weight to reduce the risk of gastrointestinal disease.