Background Data on the epidemiology and risk factors of altered gastrointestinal motility (AGIM) is virtually lacking for patients suffering from non-traumatic neurologic diseases and stroke. This study investigated whether patterns of AGIM differ between patients with stroke and other severe acute brain diseases. Methods Clinical records of stroke and non-stroke patients treated at a neurological intensive care unit (ICU) were reviewed at day 1–5 and at day 10 after admission. The data was analyzed for the course of enteral/parenteral nutrition and for and for signs and symptoms of gastrointestinal dysfunction. The study included data of 76 patients, 57 with stroke (stroke group, SG) and 19 with other neurological diseases (non-stroke group, NSG). Results Basic demographic as well as clinical baseline characteristics and alimentation regime were similar in both groups. At least one sign of AGIM was seen in 33/57 (58%) SG and in 15/19 (79%) NSG patients (P = 0.099). Regurgitation was significantly more frequent among patients from the NSG (P < 0.05). Subjects from the NSG also spent a higher proportion of time with at least one symptom of AGIM present (P < 0.05). Conclusions For the first time, this study investigated the prevalence of AGIM in patients suffering from severe stroke. The prevalence of disturbed gastrointestinal function was found to be high in stroke patients, but was lower than in a group of non-stroke patients with similar general disease severity and baseline characteristics.