Key pointsWhat's already known about this topic? Non‐invasive prenatal testing (NIPT) is a sensitive and risk‐free prenatal screening test for common aneuploidies. Until now, NIPT has required access to expensive next generation sequencing (NGS) sequencers, making it only accessible to large laboratories. What does this study add? This proof‐of‐concept study demonstrates that Oxford Nanopore platform, originally developed for long‐reads, can be used to sequence and analyze short cell‐free DNA (cfDNA) fragments with high efficiency and accuracy. We developed nanoNIPT for non‐invasive detection of fetal aneuploidies and sex chromosome aberrations, which enables NIPT testing without large upfront investments making it accessible in all the clinical labs around the world.