The High Taxonomic Fingerprint (HTF)-Microbi.Array is a fully validated phylogenetic microarray platform for an high taxonomic level characterization of the human gut microbiota. However, suffering from PCR-dependent biases in Bifidobacterium quantification, this tool is less appropriate when utilized for the characterization of the Bifidobacterium-dominated gut microbiota of breast-fed infants. In order to overcome this limit, here we implemented a new combined approach based on HTF-Microbi.Array and qPCR for a reliable fingerprint of the infant-type microbiota. This methodology was applied in a preliminary comparative study of the faecal microbiota of eight breast-fed infants, aged 2-6 months, and five young adults. While the adult gut microbiota was largely dominated by Firmicutes and Bacteroidetes, the infant-type community was mainly dominated by Bifidobacterium, with Enterobacteriaceae as the second dominant component. In accordance with the most recent literature in the field, the obtained microbiota fingerprints properly depicted the adult- and the infant-type microbiota, demonstrating the reliability of the HTF-Microbi.Array/qPCR combined approach in reflecting the peculiarities of the two intestinal microbial ecosystems. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.