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Colorectal cancer (CRC) screening is underutilized. To effect change, we must understand reasons for underuse at multiple levels of the health-care system. We evaluated patient, provider, and clinic factors that predict variation in CRC screening among primary-care clinics and primary-care providers (PCPs).We analyzed electronic medical record (EMR) data for 34,319 adults eligible for CRC screening, 19 clinics, and 97 PCPs in a large, academic physician group. Detailed data on potential patient, provider, and clinic predictors of CRC screening were obtained from the EMR. PCP perceptions of CRC screening barriers were measured via survey. The outcome was completion of CRC screening at the patient level. Multivariate logistic regression with clustering on clinics obtained adjusted odds ratios and 95% confidence intervals for potential predictors of CRC screening at each level.Seventy-one percentage of patients completed CRC screening. Variation in screening rates was seen among clinics (51–80%) and among PCPs (51–82%). Significant predictors of completing CRC screening were identified at all levels: patient (older age, white race, being married, primarily English-speaking, having commercial insurance plans vs. Medicare or Medicaid, and higher health-care resource utilization), provider (larger panel size of patients eligible for CRC screening), and clinic (hospital-owned, shorter distance to nearest optical colonoscopy center).Variation in CRC screening exists among primary-care clinics and providers within a single clinic. Predictors of variation can be identified at patient, provider, and clinic levels. Quality improvement interventions addressing CRC screening need to be directed at multiple levels of the health-care system.