After birth, the gastrointestinal (GI) tract undergoes vast structural and functional adaptations to be able to digest mother's milk and later, during the weaning period, solid food. Studies on germ-free animals have shown the role of the gut microbiota for stimulating GI maturation, but which groups are involved is unclear. In the present study, we administered the probiotic bacterium, Lactobacillus plantarum 299v (Lp299v), in the drinking water to pregnant and lactating rat dams until their pups had reached an age of 14 d. It was found that Lp299v colonizing the mothers were also able to colonize the pups, which had an impact on their gut growth and function. The small intestine, pancreas and liver weighed more in the 14 d-old pups born from dams exposed to Lp299v than in the control pups from dams given only water. Furthermore, the Lp299v pups showed decreased gut permeability. Despite a heavier spleen in the Lp299v pups, as compared to the control pups, no significant increase in the acute-phase protein, haptoglobin, was found. In conclusion, the results reported here clearly show that manipulating the maternal microflora by exposing expecting mothers to a Gram-positive, probiotic bacterium prior to parturition and during lactation impacts the gut growth and function in the offspring.