OBJECTIVES In clinical studies, comorbidity measurement refers to assessment of total burden of illnesses across multiple health conditions unrelated to the patients' disease under study. In non-randomized clinical studies and epidemiology studies, adjustment for comorbidity is often undertaken to ensure outcomes are not directly affected by comorbidities. This analysis compared 3 measurements of comorbidities and their effects on physical function and quality of life with data from a randomized controlled trial of adalimumab in ankylosing spondylitis (AS). METHODS Data were derived from the Adalimumab Trial Evaluating Long-Term Efficacy and Safety in AS (ATLAS). Comorbidity indices at baseline were calculated as Chronic Disease Score (CDS), number of separate prescription medications (prescription count), and number of concurrent illnesses (concurrent illness count). Medications taken specifically for the treatment of AS were excluded from the CDS and prescription medication count calculations. Univariate associations between each of the 3 indices and a physical function index (SF-36 PCS) and AS disease-specific quality of life (ASQOL) at Week 12 were assessed. Correlations with each comorbidity measurement were ascertained. Model selection (Alkaike's Information Criterion [AIC]) was used to identify the best comorbidity measure for predicting SF-36 PCS and ASQOL. RESULTS A total of 315 patients were included in the analysis. Their mean age was 42.2 years, and most were male (74.9%). At the univariate level, all 3 indices were significant predictors of SF-36 PCS score (p<0.02), However, only CDS and prescription medication count were significantly associated with ASQOL at Week 12. All 3 indices were well-correlated with each other (range 0.750–0.917). The AIC model demonstrated that CDS was the best predictor of SF-36 PCS and ASQOL. Prescription count was the second-best ranked measure for both outcomes. CONCLUSIONS The CDS is a suitable measure for comorbidity adjustment in examining physical function and quality of life for AS patients.