Clinical and demographic data in administrative disability tracking systems have the potential to support disability reduction programs. We analyzed recent Navy Physical Evaluation Board data, compared our findings with previous studies, and evaluated the quality of the case-tracking database as a public health information system. The overall rate of cases was 50% higher than in 2000 and 40% higher than the rate of new long-term group disability insurance claims. The most common diagnostic categories remain musculoskeletal disorders, injuries and poisonings, mental health conditions, and neurological syndromes. Diagnosis rates have increased in every category since 2000. The tracking system provided unprecedented timeliness and data accessibility, but fell short of its full potential as a public health tool due to poor information quality. Improved interface design and data entry processes combined with improved reporting capability will enhance its epidemiological value. Continued system improvement requires functional evaluation in conjunction with periodic data analysis.