To determine the association between body mass index (BMI), serum prostate-specific antigen (PSA) level and PSA density (PSAD) in patients with an elevated serum PSA level but a negative prostate biopsy. This retrospective study enrolled men with a negative prostate biopsy but a serum PSA level of 3.0-10 ng/ml. All men underwent anthropometric measurements, serum PSA determination and transrectal ultrasound examination. BMI was grouped according to the Asia-Pacific obesity criteria: nonobese (<25 kg/m(2)) versus obese (≥ 25 kg/m(2)). Partial correlation and linear regression models between PSA, PSAD and BMI were conducted after adjusting for age. A total of 907 men were enrolled in this study. On multivariate analyses, PSA showed no significant correlation with age or BMI, whereas PSAD had a negative correlation with age and BMI. Similar results were obtained when patients were categorized as having low (3.0 < PSA ≤ 6.5 ng/ml) or high PSA (6.5 < PSA ≤ 10.0 ng/ml) levels. PSAD, but not PSA, demonstrated a significant negative correlation with BMI. This indicates that a new strategy including PSAD rather than simple PSA levels should be adopted in the study of obesity-adjusted PSA cut-offs.