Central nervous system tumors are a major cause of morbidity and mortality in children. As tumor sequencing has become available, the World Health Organization diagnostic criteria have been refined to include genomic tumor characteristics. Additionally, therapeutic agents targeting specific molecular aberrations are increasingly being developed. Currently, the standard of care for tumor diagnosis includes invasive acquisition of tumor material for histopathology and molecular sequencing. Circulating tumor DNA has been shown to be detectable within the cerebrospinal fluid (CSF) of patients with brain and spinal cord tumors, representing a potential liquid biopsy. In this chapter, we describe our combined platform of Low-Pass Whole Genome Sequencing and targeted sequencing for CSF sample acquisition, cell-free DNA extraction, and processing with success in the detection of DNA copy number aberrations, sequence variants, and fusions, indicative of circulating tumor DNA presence. This technology is being implemented for clinical use at the Center for Personalized Medicine of Children’s Hospital Los Angeles.