Autistic people experience heightened rates of physical health problems but may also experience elevated levels of somatic symptoms (e.g. pain, headache, gastrointestinal symptoms) due to psychological factors which are common in autism. This online study sought to compare rates of somatic symptoms (Patient Health Questionnaire-15) in older adolescents and adults who were autistic (n = 51), non-autistic (n = 119) and who suspected they were autistic (n = 32), while controlling for health conditions. We investigated psychological risk factors that may predispose individuals to experience somatic symptoms, including alexithymia (General Alexithymia Factor Score), interoception (Body Awareness Questionnaire) and intolerance of uncertainty (Intolerance of Uncertainty Scale). Diagnosed autistic individuals had higher rates of alexithymia and intolerance of uncertainty. We also found higher somatic symptoms in diagnosed autistic individuals, controlling for mental and physical health. However, hierarchical regression showed that somatic symptoms were predicted by physical and mental health conditions, female gender, alexithymia, and intolerance of uncertainty, regardless of autism status. The results suggest that autistic and non-autistic individuals experience more bodily discomfort in part due to gender, physical and mental health, alexithymia, and difficulty tolerating uncertainty. Implications for mental and physical health care in autism are discussed.