The high mobility group A (HMGA) chromatin architectural transcription factors are a group of proteins involved in development and neoplastic transformation. They take part in an articulated interaction network, both with DNA and other nuclear proteins, organizing multimolecular complexes at chromatin level. Here, we report the development of a novel in vitro strategy for the identification of HMGA molecular partners based on the combination of an RP‐HPLC prefractionation procedure, 2‐DE gels, blot‐overlay and MS. To demonstrate that our approach could be a reliable screening method we confirmed a representative number of interactions in vitro by GST pull‐down and far‐Western and in vivo by co‐affinity purification. This approach allowed us to enlarge the HMGA molecular network confirming their involvement also in non‐transcriptional‐related processes such as RNA processing and DNA repair.