Previous studies of quality of life (QOL) note compromised QOL after stem cell transplantation (HCT), but do not usually consider the impact of pre-transplantation deficits in QOL on post transplantation outcomes. To examine these associations, multivariate models for six self-reported QOL outcomes at 6 and 12 months were constructed, considering pre-transplantation clinical status and QOL, and subsequent clinical events. Outcomes measured overall subjective health, social functioning and agreement with statements such as 'Life has returned to normal.' Of 320 autologous and allogeneic HCT recipients who completed pre-transplantation surveys, 197 completed 6-month surveys and 175 completed 12-month surveys. Pre-transplantation overall health and mental health were independent predictors of all QOL outcomes at 6 months. Baseline physical health was also predictive of four of six outcomes at 12 months. In contrast, disease risk was predictive only of enjoying normal activities at 6 months. Relapse and chronic graft-versus-host disease were associated with poorer QOL. In conclusion, pre-transplantation self-reported physical and mental health are more strongly associated with QOL after HCT than commonly noted baseline clinical predictors such as age and disease risk. Measurement of baseline QOL can help place the effects of the transplantation procedure in context.