Background: Several studies have focused on the effects of dietary inulin on the intestinal microbiota of weaned piglets. In the present study, inulin was added to a diet for gestating and lactating sows, expecting not only effects on the faecal microbiota of sows, but also on the bacterial cell numbers in the gastrointestinal tract of their piglets during the suckling period. Sows were fed a diet without (n = 11) or with (n = 10) 3% inulin, and selected bacterial groups were determined in their faeces ante and post partum. Suckling piglets, 8 per group, were euthanised on day 10 after birth to analyse digesta samples of the gastrointestinal tract. Results: Dietary inulin increased the cell numbers of enterococci, both, in the faeces of the sows during gestation and lactation, and in the caecum of the piglets (P ≤ 0.05). Moreover, higher cell numbers of eubacteria (stomach) and C. leptum (caecum), but lower cell numbers of enterobacteria and L. amylovorus (stomach) were detected in the digesta of the piglets in the inulin group (P ≤ 0.05). Conclusions: In conclusion, inulin seems to have the potential to influence the gastrointestinal microbiota of suckling piglets through the diet of their mother, showing the importance of the mother-piglet couple for the microbial development. Early modulation of the intestinal microbiota could be especially interesting with regard to the critical weaning time.