In modern pediatric emergency medicine, biomarker-based assays that enable quick bedside diagnostics and subsequent disease management can be valuable. There is a growing need for novel, disease-specific biomarkers that can improve the outcome of pediatric infectious diseases commonly encountered in the emergency department (ED). Viral respiratory infections, central nervous system infections, sepsis, and septic shock are acute disease states frequently encountered in the ED. In this review, we describe a host of novel biomarkers, including a diverse set of cytokines, chemokines, and nitric oxide–based metabolites. Based on disease pathophysiology, a rationale is provided for a molecular- or biomarker-based approach in the ED. Throughout this review, emphasis is placed on diagnostic rapidity because this relates directly to timeliness and quality of care in a busy ED. Once the biomarkers become more clinically available, in a rapid ED setting as bedside point-of-care assays, quality of care will be enhanced, not only by means of diagnostics but also in prognosticating severity of illness.