Cell-free DNA (cfDNA) sequencing with Nanopore technology represents a revolutionary approach to interrogate the genetic information present in circulating DNA, often extracted from blood plasma. Unlike traditional sequencing methods, this protocol allows for the direct sequencing of cfDNA without the need for intermediate steps such as PCR amplification or conversion and allows the analysis in real time of the methylation status of circulating cfDNA. Its applications extend to clinical diagnostics, providing valuable information for personalized medicine and disease monitoring such as liquid biopsy for cancer detection, monitoring treatment response, and identifying minimal residual disease.