Objective: Generic, preference-based health-related quality of life (HRQoL) instruments is increasingly used in health-care decision-making process. However, to our knowledge, no such HRQoL instrument has been validated or used in chronic prostatitis. We therefore aimed to assess and compare the psychometric properties of EuroQol (EQ-5D) and Short Form 6D (SF-6D) among chronic prostatitis patients in China. Methods: Consenting patients were interviewed using EQ-5D and SF-6D. Convergent and discriminative construct validities were examined with five and two a priori hypotheses, respectively. Sensitivity was compared using receiver operating characteristic (ROC) curves and relative efficiency (RE) statistics. Agreement between instruments was assessed with intra-class correlation coefficients and Bland-Altman plot, while factors affecting utility difference were explored with multiple liner regression models. Results: In 268 subjects, mean (SD) EQ-5D and SF-6D utility scores were comparable at 0.73 (0.15) and 0.75 (0.10), respectively. Five of the seven hypotheses for construct validity were fulfilled in both instruments. The areas under ROC of them all exceeded 0.5 (P < 0.001). SF-6D had 9.7-19.9% higher efficiency than EQ-5D at detecting the difference in chronic prostatitis symptom severity. Despite no significant difference in utility scores between two instruments, lack of agreement was observed with low intraclass correlation coefficient (0.218-0.630) and Bland-Altman plot analysis. Chronic prostatitis symptom severity significantly (P < 0.05) influenced differences in utility scores between EQ-5D and SF-6D. Conclusions: Both EQ-5D and SF-6D are demonstrated to be valid and sensitive HRQoL measures in Chinese chronic prostatitis patients, with SF-6D showing better HRQoL dimension coverage, greater sensitivity, lower ceiling effect, and more rational distribution. Further research is needed to determine longitudinal response and reliability.