The aim of this prospective, descriptive cohort study is to describe the prevalence of lower bowel dysfunction, possible relationship to diagnosis and severity, use of laxatives, and defecation patterns in patients with acquired brain injury during inpatient rehabilitation. Enrollment consisted of all patients admitted to an inpatient rehabilitation hospital (n = 98) within a 3-month period and assessments of fecal incontinence and fecal constipation at admission were performed. Documentation of used laxatives, number of defecations, and the macroscopic form during 4 weeks was conducted. Analysis of variance and Kruskal–Wallis analyses were conducted using the statistical software package STATA v 12/IC. At admission 75% of the patients suffered from lower bowel dysfunction, which was related to the severity of injury and age but not major diagnosis or gender. Of these, 68% suffered from fecal incontinence and 32% from fecal constipation. Ninety percent of the patients received laxatives during the initial 28 days. After 28 days, 20% continued to receive laxative treatment. There was no difference between weekly defecations in patients who had functional constipation and patients who had no bowel dysfunction. There was a strong relationship between bowel dysfunction status and prescribed laxative treatment. These findings indicate that lower gastrointestinal dysfunction is a long-lasting, profound complication following an acquired brain injury.