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Comorbidity with various health conditions is common in environmental intolerances (EIs), which restricts understanding for what symptoms that are associated with the intolerance per se. The present objectives were to study (i) prevalence of a broad range of specific symptoms in chemical, building-related, electromagnetic field- (EMF) related, and sound EI, irrespective of comorbidity, (ii) prevalence of symptoms in body systems in exclusive EIs, and (iii) increased risk of symptoms in body systems in exclusive EIs that cannot be referred to functional somatic syndromes, inflammatory diseases or mental disorders. Cross-sectional data (n = 4941) were used from two combined population-based surveys, the Västerbotten (Sweden) and Österbotten (Finland) Environmental Health Studies. Categorization of EI cases and controls were based on self-reports. Symptoms were assessed with the Environmental Hypersensitivity Symptom Inventory, and these were converted to 27 symptoms of the International Classification of Primary Care, 2nd edition, in eight chapters of body systems. The results showed, with few exceptions, that all assessed specific symptoms were significantly more prevalent in all four EIs than in referents. Although a large overlap between EIs, characteristic body system symptoms were eye and respiratory symptoms in chemical and building-related intolerance, skin symptoms in EMF-related intolerance, and general and unspecified, digestive, eye, cardiovascular, neurological, and psychological symptoms in sound intolerance. After controlling for various comorbidities, all studied body system symptoms were positively associated with chemical intolerance, fewer with sound intolerance, only one with building-related intolerance, and none with EMF-related EI. In conclusion, a broad range of symptoms are reported in all four EIs implying common mechanisms, but symptoms of certain body systems are more likely to be reported in a certain EI that cannot be explained by comorbidity.