Zonulin is considered a biomarker of increased intestinal permeability, and elevated levels have been found in celiac disease. The primary aim of this study was to examine the association between serum zonulin levels and gastrointestinal (GI) symptoms, and secondarily, between zonulin levels and anthropometric and metabolic factors. The offspring (n = 363) of the participants of the Malmo Diet and Cancer cardiovascular cohort (MDC-CV) were invited to an anthropometric and clinical examination, where fasting plasma glucose levels were measured. Questionnaires about lifestyle factors and medical history were completed along with the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Zonulin levels were measured in serum by ELISA. Neither GI symptoms nor GI diseases had any influence on zonulin levels. Higher zonulin levels were associated with higher waist circumference (p = 0.003), diastolic blood pressure (p = 0.003), and glucose levels (p = 0.036). Higher zonulin levels were associated with increased risk of overweight (p < 0.001), obesity (p = 0.047), and hyperlipidemia (p = 0.048). We cannot detect altered zonulin levels among individuals reporting GI symptoms or GI diseases, but higher zonulin levels are associated with higher waist circumference, diastolic blood pressure, fasting glucose, and increased risk of metabolic diseases.