Enteric diseases frequently occur in rabbits around weaning leading to extensive use of antibiotics. Feed restriction is a strategy routinely used to protect rabbit health during rearing. The objectives were (1) to study the impact of enteropathogens (EPEC) on the balance of the rabbit gut microflora and (2) to study the effect of feed restriction on the infection level. Rabbits (Hycole strain) were divided into 4 groups (n = 45/group) considering two factors at two levels. The first factor was the infection and the second the intake level (ad libitum vs. restricted at -25% of the voluntary feed intake). The infection was carried out at 31 days old (3 days post weaning) by oral inoculation of Escherichia coli 0128:C6. The excretion of total E. coli was quantified, ileal and ceacal bacterial communities were monitored by a fingerprint method (CE-SSCP), and ileal morphometry was also evaluated. Diarrheas were observed between 3-6 days post inoculation (pi), the higher number of morbid animals was recorded 4 days pi. The peak of excretion was detected 6 days pi. The higher effect of the infection on bacterial community structure was detected 5-7 days pi. The infection had a significant impact on ileal bacterial community, differences (t-test) between profiles (uninfected vs. infected) were 38%. Feed restriction had a weak but significant impact (7%) on ceacal infected bacterial community. No effect of feed restriction on the intestinal microbial structure was detected in healthy rabbits. At 6 days post infection, the villus height was decreased by 25% in the infected group whereas no parameter of ileal morphometry was modified by feed intake level. The resilience of the ileal bacterial community at 12 days pi was faster with a feed restriction.