The assessment of graft-versus-host disease (GVHD) as an end-point in clinical trials requires subjective judgement to distinguish morbidity caused by GVHD from morbidity caused by other complications. We developed a method based on ordinal regression for longitudinal assessment of morbidity involving the skin, liver and gut, regardless of cause as an objective end-point in randomized prospective phase III treatment or prevention trials for which GVHD is an outcome of interest. This method was validated for treatment studies by showing that morbidity was more severe among patients with grade II-IV GVHD than among those who did not have GVHD. We found no differences in morbidity involving the skin, liver and gut after the diagnosis of GVHD in a group of 30 patients who received peripheral blood stem cells and a group of 37 who received marrow in a randomized phase III clinical trial. These preliminary results suggest that objective end-points could be used in randomized clinical trials for treatment of GVHD. Further studies will be needed to determine if similar methods could be used in randomized clinical trials for prevention of GVHD.