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. Lay abstract Autistic people have more physical health problems than non-autistic people. We were interested in whether autistic people experience more discomfort in their bodies than non-autistic people and whether certain psychological traits contribute to that. A survey was completed online by older adolescents and adults, 51 of whom were autistic, 32 of whom thought they might be autistic but were not diagnosed and 119 who were not autistic. They completed measures of somatic symptoms (daily experience of pain, discomfort, dizziness), alexithymia (difficulty identifying and expressing feelings), interoception (how much people are aware of their bodies) and intolerance of uncertainty (how people handle doubt or uncertainty), and reported any physical or mental health conditions. We found that the autistic participants had more physical and mental health conditions than the non-autistic participants, but even when we took account of this, they experienced higher levels of somatic symptoms. We looked at which psychological factors influenced levels of somatic symptoms across the whole sample, and found that alexithymia, intolerance of uncertainty, having physical health problems, being female and the number of mental health conditions predicted somatic symptoms, while interoception and autism diagnosis did not. The findings suggest that people may be more likely to experience physical discomfort if they are female, and have difficulty identifying and expressing feeling and difficulty tolerating doubt. As these psychological factors are more prominent in autism, we think this is important for physical and mental health providers to know about, so that these psychological factors can be considered when assessing and treating autistic people.