The impact of an altered bacterial colonization on gut development has not been thoroughly studied, despite the increased risk of certain diseases with a disturbed microbiota after birth. This study was conducted to determine the effect of microbial manipulation, i.e. antibiotic treatment or Escherichia coli (E. coli) exposure, of the dam on bacterial colonization and gut development in the offspring. Pregnant rats were administered either broad-spectrum antibiotics three days prior to parturition, or live non-pathogenic E. coli CCUG 29300^T one week before parturition and up to 14 days of lactation in the drinking water. Caecal bacterial levels, gut growth, intestinal permeability, digestive enzyme levels and intestinal inflammation were studied in two-week old rats. Pups from dams that were antibiotic-treated had higher densities of Enterobacteriaceae which correlated with a decreased stomach growth and function, lower pancreatic protein levels, higher intestinal permeability and increased plasma levels of the acute phase protein, haptoglobin, compared with pups from untreated mothers. Exposure of pregnant/lactating mothers to E. coli CCUG 29300^T, also resulting in increased Enterobacteriaceae levels, gave in the offspring similar results on the stomach and an increased small intestinal growth as compared to the control pups. Furthermore, E. coli pups showed increased mucosal disaccharidase activities, increased liver, spleen and adrenal weights, as well as increased plasma concentrations of haptoglobin. These findings indicate that disturbing the normal bacterial colonization after birth, by increasing the densities of caecal Enterobacteriaceae, appear to have lasting effects on the postnatal microflora which affects gut growth and function.