Dynamic and individual variability of caecal bacterial community were compared to those of hard and soft feces using capillary electrophoresis single strand conformation polymorphism (CE-SSCP). Soft and hard feces of 14 adult rabbits were weekly sampled during 5 weeks while caecal content was sampled on the 3rd (after surgery) and 5th week (after sacrifice). Bacterial communities were compared for their structure (peaks of CE-SSCP profiles analysis) and their diversity (estimation of Simpson diversity index on CE-SSCP profiles, D’). Bacterial community of caecal content, soft and hard feces presented individual variability (P<0.05 for diversity and structure). Without disturbance (1st to 3rd and 4th to 5th weeks), bacterial communities of soft and hard feces remained constant in time for diversity and structure. Sampling caecal content by surgical way greatly modified all bacterial communities (P<0.05 for diversity and structure) suggesting to find an alternative sample type to realize dynamic studies of bacterial caecal community within a same individual. The bacterial communities of the 3 types of sample were different (P<0.05), but presented a similar diversity (D’=3.96±0.48; NS). However, bacterial community of caecal content was closer to that of soft feces than that of hard feces (R of ANOSIM=0.13 and 0.24, respectively) and differed only on some peaks. Therefore, we can assume that soft feces could be used to realize dynamic studies of caecal bacterial community.