OBJECTIVES To analyse the cost and cost-effectiveness of transanal colonic irrigation (TAI) using a self-administered system compared to conservative bowel management in spinal cord injury patients seen from a German perspective. METHODS A cost effectiveness model was developed based on a randomised controlled multicentre trial conducted in 2003–2005, where 87 adult spinal cord injured patients with neurogenic bowel dysfunction were allocated to 10 weeks with either TAI or conservative bowel management. The sensitivity analysis was an extreme analysis based on confidence intervals, and estimates the results for best case and worst case scenarios. Cost variables (i.e. cost of constipation medication, treatment for urinary tract infections, products, labour of carer helping with bowel management and lost productivity of patients) were included and based on the clinical study results. Estimates of resources and unit costs were made for the German health care system. Effect variables were drawn from the same clinical trial. RESULTS When comparing outcome measures at termination, TAI significantly reduced symptoms of neurogenic bowel dysfunction. For a 2-day period, product-related costs were higher for TAI (€16 vs. €4), however, labour costs due to bowel management were lower (€6 vs. €9). For TAI, costs associated with urinary tract infections (€1 vs. €3) and patient time spent (€15 vs. €23) were reduced. Thus, the total cost to society was slightly lower when patients used TAI with a self-administered system (€38 vs. €39). The sensitivity analysis shows that costs may range from €33 to €46 for TAI and from €33 to €46 for conservative bowel management. CONCLUSIONS Transanal colonic irrigation reduces the symptoms of neurogenic bowel dysfunction and results in a slightly lower total cost to society than conservative bowel management. The total cost results were found to be robust in the sensitivity analysis.