This protocol details the steps needed to prepare cell-free DNA (cfDNA) libraries with unique molecular identifiers (UMIs). The Twist cfDNA Library Preparation Kit contains new enzymes and buffers that have been reformulated and optimized to provide best-in-class amplified, indexed libraries that can be used in whole genome sequencing (WGS) experiments or downstream with Twist target enrichments kits and sequenced on Illumina next-generation sequencing (NGS) systems. The Twist UMI Adapter System consists of Twist UMI Adapters and Twist Unique Dual Indexed (UDI) Primers. This cfDNA library preparation protocol is optimized for use with Twist target enrichment kits and should only be performed with reagents specified or their equivalents.