Deep cerebral venous system thrombosis (DCVST) is a rare variety of cerebral vein and sinus thrombosis (CVST), therefore clinical information regarding presentation, course and outcome are limited. In this twocenter study including 32 patients, we tried to better define symptoms, neuroradiological findings, course, and outcome in DCVST. All consecutive patients with DCVST admitted to our two institutions over a period of more than 10 years were identified from prospective registries on CVST and stroke patients. Data from the registries were confirmed and complemented by retrospective analysis of patients' charts and neuroradiological imaging. Only patients with an unequivocal diagnosis of DCVST confirmed by MRI and MRA were included. Information on long-term functional outcome (modified Rankin Scale, mRS; ability to return to work) was obtained by telephone interviews performed between 2006 and 2008. The clinical presentation was highly variable with headache (81%) and reduced consciousness (72%) as the most frequent symptoms. In nine patients (28%) thrombosis was confined to the deep venous system (isolated DCVST). In the remaining patients other sinuses and/or cortical veins were additionally affected (non-isolated DCVST). Diagnosis was made within one to 76 days (mean = 10.0 ± 14.1 days) but was significantly delayed in patients with isolated compared to non-isolated DCVST (19.1 ± 23.0 vs. 6.3 ± 6.5 days, P = 0.02). Thalamic edema was the most frequent parenchymal MRI finding present in 69% of patients, bilateral in 47%. D-dimer levels were normal in 13% of patients. Most patients (75%) stabilized and later improved on intravenous heparin or subcutaneous low molecular weight heparin. Eight (25%) patients deteriorated with progressing coma; six of them received local endovascular therapy but two died. After a mean follow- up of 3.8 years (range 3 months-13 years), 26 patients (81%) were functionally independent (mRS B 2) including 24 patients (75%) with a mRS B 1 of whom 23 (96%) returned to their previous job, activity or education. No patients were severely disabled (mRS 4-5). Extension of thrombosis beyond the deep venous system had no effect on outcome. Due to its variable clinical presentation the diagnosis of DCVST is often difficult and heparin treatment therefore established with substantial delay. While most patients stabilize and have a good recovery, progressing coma associated with poor outcome is seen in a subset of patients who may thus require other treatment options, such as endovascular therapy.