Based on the concept of central sensitisation, the present study tested the hypothesis of comorbidity in allergic asthma and allergic rhinitis with diagnoses of functional somatic syndromes (FSSs), including fibromyalgia, irritable bowel syndrome and migraine. Data were used from the population-based Västerbotten Environmental Health Study (n = 3406). The participants consisted of 164 individuals with allergic asthma and 298 individuals with allergic rhinitis as well as 2876 individuals without allergic or non-allergic asthma, allergic rhinitis or atopic dermatitis. Diagnoses were based on self-reports of having been diagnosed by a physician. Odds ratios (ORs) were calculated from binary logistic regression analysis, both crude and adjusted for age and education. The adjusted ORs (1.87–4.00) for all FSSs differed significantly from unity for both allergic asthma and rhinitis. The results provide support for the hypothesis of comorbidity in allergic asthma and rhinitis with FSSs. Since central sensitisation is likely to underlie FSSs, the present findings raises the question as to whether central sensitisation may also be involved in allergic asthma and rhinitis.