The purpose of this study was to examine longitudinally health-related quality of life (HRQOL) and related factors in mothers and fathers of children who undergo SCT, before, and 1 and 2 years after SCT. A total of 84 parents (49 mothers/35 fathers) of patients diagnosed mainly with leukemia completed a HRQOL measure before SCT, 46 at 1 year (26 mothers/20 fathers) and 50 parents (31 mothers/19 fathers) at 2 years post SCT. Physical and psychosocial HRQOL summary scores are reported. Parents' age and gender, child's diagnosis, radiation history, age, behavior and physical health were examined. Linear mixed models for repeated measures with a covariate structure were used for analysis. Physical HRQOL did not differ between mothers and fathers or over time. Maternal and paternal psychosocial HRQOL scores improved by 2 years post SCT. Child's behavior problems and poor health, and maternal age (younger) predicted poor maternal psychosocial HRQOL 2 years post SCT. Child's behavior problems, diagnosis and treatment severity predicted poor paternal psychosocial HRQOL. These findings identify similar (child's poor behavior) and differential risk factors (parental young age, disease and treatment severity, and child's poor health status) for poor HRQOL for mothers and fathers. These findings can guide comprehensive family-care interventions before, during and after pediatric SCT.