While developed for managing individuals with atrial fibrillation, risk stratification schemes for stroke, such as CHADS2, may be useful in population-based studies, including those assessing process of care. We investigated how certain decisions in identifying diagnoses from administrative data affect the apparent prevalence of CHADS2-associated diagnoses and distribution of scores. Two sets of ICD-9 codes (more restrictive/ more inclusive) were defined for each CHADS2-associated diagnosis. For stroke/transient ischemic attack (TIA), the more restrictive set was applied to only inpatient data. We varied the number of years (1-3) in searching for relevant codes, and, except for stroke/TIA, the number of instances (1 vs. 2) that diagnoses were required to appear. The impact of choices on apparent disease prevalence varied by type of choice and condition, but was often substantial. Choices resulting in substantial changes in prevalence also tended to be associated with more substantial effects on the distribution of CHADS2 scores.