Foodborne illness (FBI) is a preventable economic and public health burden yet continues to be a major problem in the United States. It is estimated that 48 million FBI cases occur each year. Routine inspections of food facilities conducted by public health inspectors are the principal method for ensuring food safety, and through these inspections data is routinely collected. Analysis of these inspections may produce information useful in targeting prevention efforts. The objective of this study was to determine the characteristics of food facilities that are associated with food safety violations, especially facility size and risk level. Retrospective routine inspection data for the years 2013 and 2014 from the San Diego County Department of Environmental Health was examined A total of 43,194 inspections were conducted during this time which resulted in 112,145 violations. The predictors examined were business types, facility size, and facility risk classification to determine association with violation frequencies. The violations from this data were also analyzed in comparison to the top five Centers for Disease Control and Prevention (CDC) risk factors for FBI. Compared to the other facilities, restaurants had a higher frequency of violations than expected for four out of the five CDC risk factors which included improper hot/cold holding temperatures, improper cooking temperatures, dirty and/or contaminated utensils and equipment, and poor employee health and hygiene. Miscellaneous food facilities, pre-packaged retail market, and retail market with deli all had higher frequency of food from unsafe sources than expected. By size, small sized facilities in the medium-risk category had a higher frequency than expected for improper hot and cold holding temperatures of potentially hazardous food and poor employee health and hygiene. High-risk facilities were more likely to be ordered closed or have major violations. More than half of all facilities (60.7%) were repeat violators (>1 violation per unique inspection). This data indicates that medium-risk small sized facilities should potentially be a target for FBI outreach and prevention efforts, as well as continuing efforts directed towards high-risk facilities, especially restaurants.