Irritable bowel syndrome patients often complain of urinary symptoms such as frequency, urgency, and dysuria, raising the possibility of inappropriate referral to the urologist. To resolve this issue, the prevalence of irritable bowel syndrome was compared in patients attending urological and control clinics (dermatology and ENT). The overall prevalence of irritable bowel syndrome was 31.2% in the urological clinic compared with 21.2% in the controls (P < 0.001), but striking, differences emerged, depending on presenting complaint. Irritable bowel symptoms were particularly common in patients presenting with loin pain (male: 40.9%, P = 0.004; female: 50%, P = 0.03), dysuria (male: 43.8%, P = 0.007; female: 46.2%, P = 0.01) and frequency/urgency (male: 31.7%, P = 0.002; female: 42.4%, P = 0.006), and the male/female prevalence was 24% and 44%. These results suggest that in irritable bowel syndrome, urinary symptoms including loin pain can present diagnostic dilemmas in both the gastroenterological and urological setting, underlining the importance of specialists in these fields working together in order to define better ways of managing such patients.