Due to their large diversity with respect to post-translational modifications (PTMs), the family of histones provides a major analytical challenge in current proteomics research. Their function has a large impact on the transcription of DNA, and as a result, on the expression of proteins. The variation in PTMs regulates transcription, and, as a result, many methods are being employed for the in-depth analysis of histones. In this paper, we present a separation strategy for histones based on free-flow electrophoresis (FFE) followed by an RP separation on capillary monolithic PS-DVB columns. The capillary columns are directly interfaced with an FT-ICR MS providing an online system for the detection and accurate molecular weight analysis of intact histones.