INTRODUCTION: Population-based surveys are used to assess colorectal cancer (CRC) screening rates, but may be subject to self-report biases. Clinical data from electronic health records (EHR) are another data source for assessing screening rates and self-report bias; however, use of EHR data for population research is relatively new. We sought to compare CRC screening rates from a self-report survey, the 2007 California Health Interview Survey (CHIS), to EHR data from Palo Alto Medical Foundation (PAMF), a multi-specialty healthcare organization serving three counties in California. METHODS: Ever- and up-to-date CRC screening rates were compared between CHIS respondents (N=18,748) and PAMF patients (N=26,283). Both samples were limited to English proficient subjects aged 51-75 with health insurance and a physician visit in the past two years. PAMF rates were age-sex standardized to the CHIS population. Analyses were stratified by racial/ethnic group. RESULTS: EHR data included PAMF internally completed tests (84%), and patient-reported externally completed tests which were either confirmed (7%) or unconfirmed (9%) by a physician. When excluding unconfirmed tests, PAMF screening rates were 6-14 percentage points lower than CHIS rates, for both ever- and up-to-date CRC screening among Non-Hispanic White, Black, Hispanic/Latino, Chinese, Filipino and Japanese subjects. When including unconfirmed tests, differences in screening rates between the two data sets were minimal. CONCLUSION: Comparability of CRC screening rates from survey data and clinic-based EHR data depends on whether or not unconfirmed patient-reported tests in EHR are included. This indicates a need for validated methods of calculating CRC screening rates in EHR data.