Summary Chronic lymphocytic leukaemia (CLL) remains the most common incurable malignancy of B cells in the western world. Patient outcomes are heterogeneous and can be difficult to predict with current prognostic markers. Here, we used a quantitative label‐free proteomic technique to ascertain differences in the B‐cell proteome from healthy donors and CLL patients with either mutated (M‐CLL) or unmutated (UM‐CLL) IGHV to identify new prognostic markers. In peripheral B‐CLL cells, 349 (22%) proteins were differentially expressed between normal B cells and B‐CLL cells and 189 (12%) were differentially expressed between M‐CLL and UM‐CLL. We also examined the proteome of proliferating CLL cells in the lymph nodes, and identified 76 (~8%) differentially expressed proteins between healthy and CLL lymph nodes. B‐CLL cells show over‐expression of proteins involved in lipid and cholesterol metabolism. A comprehensive lipidomic analysis highlighted large differences in glycolipids and sphingolipids. A shift was observed from the pro‐apoptotic lipid ceramide towards the anti‐apoptotic/chemoresistant lipid, glucosylceramide, which was more evident in patients with aggressive disease (UM‐CLL). This study details a novel quantitative proteomic technique applied for the first time to primary patient samples in CLL and highlights that primary CLL lymphocytes display markers of a metabolic shift towards lipid synthesis and breakdown.