Our aim was to establish the Estonian version of the National Institutes of Health chronic prostatitis symptom index (NIH-CPSI), and to examine its validity and applicability in chronic prostatitis patients as well as in community-based study. The questionnaire was tested in 54 category III prostatitis patients. In addition, 452 men were enrolled into a community-based study that resulted in 83 completed questionnaires. The discriminatory power, psychometric properties and internal correlations of the questionnaire were tested. The questionnaire demonstrated good internal consistency, with Cronbach's alpha coefficient 0.82. The pain and quality of life domains demonstrated high correlations with each other and with the entire questionnaire. The total score and the scores of pain and quality of life domains of the Estonian NIH-CPSI differed significantly between the chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) patients and the men without CP/CPPS, and so the index proved a good discriminant validity. We can conclude that the Estonian NIH-CPSI is easily understood and reflects accurately the clinical symptoms and the quality of life in patients with chronic prostatitis. The similarity of the psychometric properties of the English and Estonian versions of the NIH-CPSI supports their measurement equivalence.