It is reported that some, but not all, bacteria in human faeces are coated with secretory immunoglobulin A (S-IgA). We evaluated the proportion of S-IgA-coated bacteria to total intestinal bacteria (S-IgA coating ratio) in the gastrointestinal tract of two different strains of mice supplied by two different suppliers. The S-IgA coating ratio was significantly different in each gastrointestinal segment and between mouse suppliers. The amount of non-bacteria-bound IgA (free IgA) in each gastrointestinal segment indicated that this difference in the S-IgA coating ratio might not be due to the amount of secreted IgA. Furthermore, immunoblotting analysis revealed that only a small amount of IgA (<5% to free-IgA) was used for the coating. This indicates that, although sufficient S-IgA was secreted to coat the entire intestinal population of bacteria, only some part of the bacteria were coated with S-IgA. This study suggests that the amount of luminal S-IgA may not determine the S-IgA coating ratio, and that the amount of IgA coating intestinal commensal bacteria is very small.