Introduction: This paper presents an option for evaluating food control effectiveness by analysing the frequency of non-compliances (FnC). Material and methods: A food business establishment can have several different types of control areas (i.e. pest control, HACCP), that can be inspected to assess its compliance with regulations in the food sector. From April 2012 to April 2014, 10 736 inspections were performed in Sweden, covering all 15 types of control areas. In these inspections, 2223 noncompliances were found, giving a FnC of 0.21 per control area inspected. Outlying types of control areas, inspection teams and establishments were selected for supervision of the internal audit procedure. Results and discussion: The key and surprising finding was that types of control area, teams and establishments with high FnC had a higher ratio of false negative non-compliances than those with low FnC. Moreover, false negative non-compliances were more common than false positive non-compliances. Possible explanations include the complexity of legislation affecting food businesses and the complexities of the food business. Conclusions: The risk of non-compliance going undetected is greatest where many noncompliances have already been detected. These results should inform future food control strategies.