Major differences have been found in gut microbiota between healthy and allergic children, and a possible association between allergy and altered microbiota patterns have been postulated. The main object of the study was to compare the faecal microbiota between healthy and cow’s milk protein allergy (CMPA) infants at the baseline immediately after the diagnosis, and to evaluate the changes in the faecal microbiota after 6 months of treatment of CMPA infants fed on extensively cow’s milk protein hydrolyzed formulae without pre- or probiotics, compared with healthy children fed on standard milk formulae. The population comprised 92 infants aged 2-12 months who were non-allergic (n = 46) or diagnosed with IgE-mediated CMPA (n = 46). At baseline and at 6 months, faecal samples were collected into sterile plastic tubes, immediately placed into anaerobic jars and processed within 2 h of their collection. Weighed faeces samples were diluted from 10(-1) to 10(-7) and cultured in selective media for total count of aerobes, anaerobes, enterobacteria, bifidobacteria, lactobacilli, clostridia and yeasts. Samples from non-allergic and allergic infants were compared at baseline and at 6 months using appropriate statistical tests, considering p < 0.05 to be significant. In comparison with healthy infants, CMPA infants had higher total bacteria and anaerobic counts and a lower yeast count at baseline, finding no difference in the proportions of each bacterial group between groups. After 6 months, CMPA infants showed higher anaerobic and lactobacilli counts, a higher proportion of lactobacilli, a lower count and proportion of bifidobacteria, and lower proportions of enterobacteria and yeasts. Comparison of faecal samples from CMPA infants between baseline and at 6 months showed an increase in count and proportion of lactobacilli and a decrease in counts and proportions of enterobacteria and bifidobacteria. Differences in the composition of gut microbiota between CMPA and healthy infants may influence in the development of or protection from this allergy.