To describe the extent and distribution of in patient costs of nontraumatic lower limb amputations and to identify areas of high cost as a basis for cost saving strategic planning.Retrospective review of 134 consecutive admissions resulting in lower limb amputations for reasons other than trauma over a 33 month period. General surgical and orthopaedic costs were compared. More detailed cost distribution analysis was then conducted for a group of general surgical amputees corroborating data from the resource utilisation system, Otago surgical audit and patient records.The mean cost of admission for nontraumatic lower limb amputations performed by general surgeons was $11,342 (median $21,439 range $144-$43,022) and was significantly more expensive than orthopaedic amputations, mean $2318 (median $6277 range $307-$13,907) p < 0.001. Of general surgical patients, 38.7% had diabetes and these accounted for 36.1% of total costs. Most amputations (73.9%) in diabetics were of the minor type compared with 29.0% in the nondiabetic group (p < 0.001). Ward costs accounted for the largest proportion of total cost 55.6% (95% CI 45.1, 66.0). For major amputees 40% (95% CI 31.4, 48.1) of in-hospital time was used for rehabilitation.Nontraumatic amputations are costly. Diabetics, having mainly minor amputations, account for a disproportionate amount of the cost. Length of hospital stay is the most important determinant of cost, much of which is spent on rehabilitation. A case is made for early definitive surgery and a greater use of community based services and low cost centres in rehabilitation.