OBJECTIVES: The Child Health Utility-9D (CHU9D) and Assessment of Quality of Life-6D (AQOL-6D) currently represent the only two generic preferences based instruments developed for application in the economic evaluation of new health technologies with both adult and adolescent specific scoring algorithms attached to them. The main objective of this study was to compare and contrast the application of adult and adolescent scoring algorithms for the CHU9D and AQOL-6D in valuing the health of a community based sample of adolescents. METHODS: A web based survey including the CHU9D and the AQOL-6D was developed for administration to adolescents residing in Australia, aged 11-17 years (n=500). Individual responses to both instruments were converted to health state utility values by applying [1] adult and [2] adolescent scoring algorithms pertaining to each instrument.  RESULTS: Both the AQOL-6D and CHU9D discriminated well according to health status and long standing illness regardless of the scoring algorithm employed. However, important discrepancies were found in that employment of the adolescent algorithm resulted in consistently lower mean health state values for the CHU9D but consistently higher mean health state values for the AQOL-6D relative to employment of their respective adult algorithms and these differences were found to be statistically significant for both instruments (p<0.05). CONCLUSIONS: The findings from this study concur with an expanding evidence base highlighting discrepancies in adult and adolescent values for identical health states. The differences in adolescent and adult values were more profound for the CHU9D, particularly in relation to mental health impairment states, and may be significant enough to strongly affect the findings of cost effectiveness studies and ultimately health care policy.  There are important differences between both the CHU9D and AQOL-6D descriptive systems and the methods of valuation utilized for each instrument which may impact on the health state utility values generated by each scoring algorithm.