CUT&RUN is an antibody-targeted nuclease-cleavage method that profiles the genome-wide occupancy of DNA-binding proteins, histones and chromatin modifying proteins\u00a0in situ with exceptional sensitivity and resolution. Here we provide a protocol to perform CUT&RUN in an automated 96 well format using a Beckman Biomek FX liquid handling robot equipped for magnetic separation and temperature control. To circumvent the need to purify small amounts of DNA prior to library preparation, we developed a method to polish the DNA ends in chromatin fragments for direct ligation of Illumina library adapters. This allows the samples to be kept in a 96 well format throughout the DNA end-polishing and adapter ligation steps. Deproteinated CUT&RUN libraries are purified on the Biomek using Ampure XP magnetic beads both before and after PCR enrichment. This AutoCUT&RUN protocol allows a single operator to generate up to 96 libraries in two days that are ready to be pooled and sequenced. The easy, cost-effective workflow makes AutoCUT&RUN an attractive tool for high-throughput characterization of chromatin features, and because AutoCUT&RUN generates high-quality profiles from frozen tissue samples this method is also suitable for rapidly profiling the epigenetic content of patient samples.