Despite the important role of the microbiota in the human gastrointestinal tract (GIT) and its impact on life-long health, the successional process through which this microbial community develops during infancy is still poorly understood. Specially, little is known about how the amount and type of viruses present in the GIT, i.e., the virome, varies throughout this period and about the role this collection of viruses may play in the assembly of the GIT microbiota. The patterns of taxonomic change of the GIT viral community can be analyzed in a birth cohort of infants during the first year of life. The present chapter presents a detailed protocol for the isolation and extraction of viral nucleic acids from collected human faecal samples, whole genome amplification (WGA) using phi29 DNA polymerase and preparation for sequencing through high-throughput 454 pyrosequencing. The sequencing data can be posteriorly used for taxonomic classification in order to establish the composition of the virome present in each sample and to assess the process of viral dynamics through time.