Equine herpesvirus-2 (EHV-2) infection has been implicated as a cause of a variety of clinical disorders in young horses, including upper respiratory tract disease, generalized malaise, fever, pharyngeal lymphoid hyperplasia, and lymphadenopathy. Considerable sequence heterogeneity has been demonstrated previously among EHV-2 strains, and individual horses can be concurrently infected with more than one virus strain. In this study, the temporal variation of the viral load and genomic diversity of the glycoprotein B (gB) gene of EHV-2 in the nasal secretions of a cohort of foals was characterized during the first 5 months of life. The viral load in nasal secretions of foals peaked when the foals were approximately 3 months old, and there was notable genetic heterogeneity of the gB gene, both among foals and within individuals. Furthermore, there was evidence of positive selection of EHV-2 variants with unique amino acid sequences at specific sites of gB.