Cerebral venous sinus thrombosis (CVST) is a cerebrovascular disease characterized by thrombosis of the cerebral venous or dural sinuses. Autoimmune diseases (AD) are important causes of CVST. This study aims to reveal the differences between CVST associated with autoimmune diseases compared with other causes (OCs) and Behcet's syndrome (BS) compared with other ADs. This is a single-center retrospective study in which the medical records of 187 patients we followed with a diagnosis of CVST between 2008 and 2023 were collected retrospectively. Four neurologists collected data on initial symptoms, neurological examinations, and laboratory findings. Findings on magnetic resonance imaging and magnetic resonance venography performed on all patients (thrombosis localizations, hemorrhagic or ischemic complications, and collateralization) were re-evaluated by 2 radiologists. The results were compared with AD, other ADs, and OCs groups. There were 28 cases of CVST associated with AD. Of these, 18 were BS, and 10 were other AD. Subacute-chronic onset, headache, and transverse sinus involvement were more common in AD-related patients than in OCs. However, collateralization, venous infarction, hemorrhagic transformation, and bleeding were less common. BS-related patients had earlier age, more frequent transverse sinus, less frequent cortical vein thrombosis, and better collateralization than other ADs. CVST is one of the rare complications in autoimmune diseases. It has a more subacute-chronic onset. Since headaches are more common, it is essential to make a differential diagnosis of CVST in autoimmune diseases with chronic headaches. Transverse sinus thrombosis is more common. Collateralization, venous infarction, and hemorrhagic transformation are less.