We compared the coding of comorbid conditions in an administrative database to that found in medical records for 485 men who had undergone a prostatectomy. Only a few specific conditions showed good agreement between charts and claims. Most showed poor agreement and appeared more frequently in the chart. A comorbidity index calculated from each of these sources was used to explore the differences in mortality for patients who had undergone transurethral vs open prostatectomy. The claims-based comorbidity index most often underestimated the index from the chart. Proportional hazards analysis showed that models including either comorbidity index were better than those without an index and models with information from both indices were best. No analysis eliminated the effect of type of prostatectomy on long-term mortality. Claims-based measures of comorbidity tend to underrepresent some conditions but may be an acceptable first step in controlling for differences across patient populations.