BACKGROUND Maintenance of Certification (MOC) for Family Physicians (MC-FP) includes clinical Self-Assessment Modules (SAMs). Whether family physicians choose SAMs that reflect their aptitudes or knowledge gaps has not been studied. METHODS Secondary analysis of demographic data, 2009 certification examination scores, and 2009-2012 SAM participation data. We computed disease-specific scores for asthma, diabetes, and hypertension from the examination. We ran unadjusted logistic and adjusted conditional logistic regression models of score quintiles, matched on the number of SAMs completed and controlling for physician demographics and area-level social deprivation. RESULTS In 2009, 9,610 physicians passed the exam. Mean scores were 591.4 (SD ± 308.5) for asthma, 558.6 (SD ± 216.1) for diabetes, and 533.3 (± 226.7) for hypertension. Average scores on hypertension and diabetes were higher for physicians who subsequently completed related SAMs but not for those who completed the asthma SAM. The percentage of physicians in each quintile of scaled score who completed each SAM increased for diabetes (32.3%-40.9%) and hypertension (33.0%-36.9%). For asthma, logistic regression analyses found no statistically significant associations. For diabetes, there was a consistent association in both models between higher score quintile and likelihood of taking the SAM. For hypertension, an association of higher score and higher likelihood of taking the SAM was significant only in the third quintile (OR = 1.20 (1.03, 1.39)). CONCLUSIONS We found inconsistent relationships between physician knowledge and SAM selection. For MOC to better impact quality, boards should consider directing physicians toward MOC activities that fill knowledge gaps rather than areas of strength.