Irritable bowel syndrome (IBS) is common in ankylosing spondylitis (AS) and may be associated with the disease. We aimed to determine the prevalence of IBS in AS patients and its association with clinical and demographic patient characteristics and with macroscopic and microscopic gut lesions. Sixty consecutive AS patients were included in this study. Disease activity was assessed with the BASDAI (Bath Ankylosing Spondylitis Disease Activity Index) and functional status with the BASFI (Bath Ankylosing Spondylitis Functional Index). The ROME III criteria were used to diagnose IBS. Macroscopic lesions were graded during colonoscopies. Biopsy specimens were taken from the terminal ileum, colon (ascending, transverse and descending) and rectum. Histological samples were scored with Cuvelier grading. The prevalence of IBS was 23.3% (14/60). The mean age of 14 IBS subjects (10 male) was 32 ± 8.50., with a higher BASDAI (p = 0.046). Macroscopic lesions were more frequent in IBS cases in the terminal ileum (46.2% vs. 34.9%), ascending colon (21.4% vs. 2.2%) and rectum (21.4% vs. 17.4%), with Grade 2 significantly more prevalent in the ascending colon (p = 0.03). Microscopic lesions did not differ among the IBS-present and -absent groups. In conclusion, the prevalence of IBS was high in AS patients and associated with higher disease activity. Grade 2 macroscopic lesions were more frequent in the ascending colon.