BACKGROUND: Generic preference-based health-related quality of life instruments are widely used to measure health benefit within economic evaluation. The availability of multiple instruments raises questions about their relative merits and recent studies have highlighted the paucity of evidence regarding measurement properties in the context of spinal cord injury (SCI). This qualitative study explores the views of individuals living with SCI towards six established instruments with the objective of identifying 'preferred' outcome measures (from the perspective of the study participants). METHODS: Individuals living with SCI were invited to participate in one of three focus groups. Eligible participants were identified from Vancouver General Hospital's Spine Program database; purposive sampling was used to ensure representation of different demographics and injury characteristics. Perceptions and opinions were solicited on the following questionnaires: 15D, Assessment of Quality of Life 8-dimension (AQoL-8D), EQ-5D-5L, Health Utilities Index (HUI), Quality of Well-Being Scale Self-Administered (QWB-SA), and the SF-36v2. Framework analysis was used to analyse the qualitative information gathered during discussion. Strengths and limitations of each questionnaire were thematically identified and managed using NVivo 9 software. RESULTS: Major emergent themes were (i) general perceptions, (ii) comprehensiveness, (iii) content, (iv) wording and (v) features. Two sub-themes pertinent to content were also identified; 'questions' and 'options'. All focus group participants (n = 15) perceived the AQoL-8D to be the most relevant instrument to administer within the SCI population. This measure was considered to be comprehensive, with relevant content (i.e. wheelchair inclusive) and applicable items. Participants had mixed perceptions about the other questionnaires, albeit to varying degrees. CONCLUSIONS: Despite a strong theoretical underpinning, the AQoL-8D (and other AQoL instruments) is infrequently used outside its country of origin (Australia). Empirical comparative analyses of the favoured instruments identified in this qualitative study are necessary within the context of spinal cord injury.