Abstract Background Children with allergic diseases such as asthma and atopic dermatitis experience increased gastrointestinal symptoms. Further, physiological and histological abnormalities of the gastrointestinal tract in patients with allergic diseases have been reported. It is not certain whether adult patients experience increased gastrointestinal symptoms. Methods A retrospective, case–control study of 7235 adult (⩾20 years old) primary care patients was conducted. A general practitioner diagnosis of irritable bowel syndrome was used to serve as a marker of lower gastrointestinal symptoms. The prevalence of lower gastrointestinal symptoms was calculated in patients with asthma or allergic rhinitis and compared with that in patients with other chronic diseases (insulin-dependent diabetes mellitus, osteoarthritis and rheumatoid arthritis) and with the remaining population. Results Gastrointestinal symptoms were significantly more common in patients with asthma (9.9%) as compared with patients with chronic diseases (4.9%; odds ratio (OR) 2.13, 95% confidence interval (CI) 1.39 to 2.56; p<0.002) or the remaining non-asthmatic population (5.5%; OR 1.89, 95% CI 1.39 to 2.56; p<0.001). Gastrointestinal symptoms were also significantly more common in patients with allergic rhinitis (7.9%) as compared with patients with chronic diseases (4.9%; OR 1.66, 95% CI 1.02 to 2.7; p<0.05) and the remaining population (5.5%; OR 1.47, 95% CI 1.04 to 2.1; p<0.02). This phenomenon was independent of age, sex and inhaled asthma therapy in the case of patients with asthma. Conclusions Our findings support the hypothesis that lower gastrointestinal symptoms are more common in patients with allergic diseases such as asthma and allergic rhinitis.