Organic certification, especially for smallholders, often uses group certification procedures. An internal control system (ICS) visits all farmers, and then the external certification body (CB) inspects a sample to assess the ICS’ performance. Harmonised methods for measuring the ICS’ reliability are missing so far. Here, we define criteria of “ICS performance”, propose a new procedure for quantifying this performance and, based on this procedure, suggest that the sample size can be determined using classical statistical methods for survey sampling, instead of using the square root or a percentage of group size as in current practice.