The aim of this study was to investigate the performance of the recent EQ-5D-Y instrument compared with the standard EQ-5D in assessing the health-related quality of life of high school children in Cape Town. Either the EQ-5D or the EQ-5D-Y was given to high school children. The sample consisted of 521 respondents. The EQ-5D-Y was found to be superior in that there were statistically significant fewer missed item responses, both in the domains and the health status Visual Analogue Scale (VAS). A grade differential was noted with more missing responses in the lower grades, particularly with the EQ-5D. More children reported problems with the mobility, self-care and anxiety and depression domains when responding to the EQ-5D-Y. In addition, the mean VAS score was marginally greater using the EQ-5D-Y. The EQ-5D-Y performed better than the EQ-5D, particularly in the younger children, and should be used in early secondary school. The EQ-5D-Y generated a wider range of responses in both the domains and the VAS, and may be more responsive than the Adult version. The two seem to give different results and consequently should be considered two related but separate instruments.