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Background Pharmacy databases are commonly used to assess medication usage, and a number of measures have been developed to measure patients’ adherence to medication. An extensive literature now supports these measures, although few studies have systematically compared the properties of different adherence measures. Methods As part of an 18-month randomized clinical trial to assess the impact of automated telephone reminders on adherence to inhaled corticosteroids (ICS) among 6903 adult members of a managed care organization, we computed eight pharmacy-based measures of ICS adherence using outpatient pharmacy dispensing records obtained from the health plan’s electronic medical record. We used simple descriptive statistics to compare the relative performance characteristics of these measures. Results Comparative analysis found a relative upward bias in adherence estimates for those measures that require at least one dispensing event to be calculated. Measurement strategies that require a second dispensing event evidence even greater upward bias. These biases are greatest with shorter observation times. Furthermore, requiring a dispensing to be calculated meant that these measures could not be defined for large numbers of individuals (17-32 % of participants in this study). Measurement strategies that do not require a dispensing event to be calculated appear least vulnerable to these biases and can be calculated for everyone. However they do require additional assumptions and data (e.g., pre-intervention dispensing data) to support their validity. Conclusions Many adherence measures require one, or sometimes two, dispensings in order to be defined. Since such measures assume all dispensed medication is used as directed, they have a built in upward bias that is especially pronounced when they are calculated over relatively short timeframes (< 9 months). Less biased measurement strategies that do not require a dispensing event are available, but require additional data to support their validity. Trial registration The study was funded by grant R01HL83433 from the National Heart, Lung and Blood Institute (NHLBI) and is filed as study NCT00414817 in the clinicaltrials.gov database.