With the withdrawal of antibiotic growth promotants, a better knowledge and control of the microflora of the digestive tract is essential for animal feeding. The digestive bacterial community varies between individuals. This variability may be lower in broilers due to the increased homogeneity in animals by genetic selection. Individual variability was studied at various ages according to diet. Broilers were fed with a diet composed of wheat either ground (G) or as whole grains (W) given as free choice feeding. Caecal contents of 6 birds per diet were sampled weekly (from 16 to 44 d) to study the predominant bacterial population using a molecular fingerprinting method. Similarity coefficients (Pearson correlation method) were calculated for each pair of profiles, and were compared between diets with Student’s t-test (p ≤ 0.05). Gel profiles showed inter-individual differences. At some ages, this variability differed according to diet. At 23 d of age, inter-individual differences appeared higher with W diet than with G diet which may be due to inter-individual variability of whole wheat intake with W diet. However, at 37 and 44 d, W diet led to higher microflora homogeneity between birds than G diet. The digestive microflora of broilers showed an inter-individual variability that can be modified by diet. This variability must be taken into account when studying factors influencing microflora.