Framed in a study on the cost-effectiveness of different diagnostic strategies regarding children with meningeal signs, this study evaluated the quality weights for permanent sequelae after childhood bacterial meningitis obtained with two different classification instruments: the EQ-5D, and Health Utilities Index (HUI). A panel of 28 pediatricians classified seven standardized descriptions of patients with permanent sequelae after bacterial meningitis according to the EQ-5D and HUI classification system. Quality weights for each classification were calculated using the EQ-5D and HUI standard scoring algorithms. HUI Mark 3 quality weights were substantially lower than the EQ-5D for all descriptions (mean difference 0.11; 95% CI: 0.08-0.14). Mean Kendall W for agreement of the ranking order between EQ-5D and HUI Mark 3 was 0.90. The EQ-5D and HUI resulted in different absolute quality weights, in particular for states associated with "deafness" and "mental retardation." Due to their performance differences, the HUI may be preferable to EQ-5D in studies focussed on "sensation" (hearing, vision, speech) or "cognition." These differences proved not to be relevant in the present cost-utility study of diagnostic strategies to rule out bacterial meningitis, as such consequences were at the distal end of the decision tree. This may be different in a cost-utility analysis of therapeutic strategies. Hence, sensitivity analysis to quality weights is recommended.