Neonatal diarrhea in suckling and weaned piglets is a prevalent disease within the pig farms. It generates considerable economic losses associated with mortality, treatments, productivity reduction and delayed growth. The mortality rates are high in piglets from 1 to 8 weeks of age, although frequently between the 1st and 4th week of age. The etiological agents involved include: Porcine Epidemic Diarrhea Virus (PEDV), rotavirus (RV), Mamastrovirus, among others. The aim of the present research is to analyze phylogenetically the PEDV and RV from fecal samples collected from pigs farms located in Cundinamarca, Colombia to study| the evolution and genetic diversity of the strains present in the country. Materials and methods. The methodology will include the identification of PEDV and RV in fecal specimens of piglets up to 6 weeks of age, through viral RNA extraction and reverse transcription-PCR amplification (RT-PCR). Confirming the presence of the viruses of interest, the genome will be sequenced using the Next Generation Sequencing (NGS) platform from Miseq (Illumina®). Expectations: Providing information on the evolution and genetic diversity of PEDv and RV strains in Colombia, through the NGS sequencing of viral genomes identified with RT-PCR in young piglets with diarrhea.