In renal transplantation, the presence of anti-donor HLA antibodies is associated with early rejection and accelerated graft loss. The clinical relevance of anti-HLA antibodies can be evaluated in the crossmatch assay using either a complement-dependent cytotoxicity (CDC) assay or a flow cytometric crossmatch (FCXM) method. The FCXM technique is more sensitive than CDC-based assays for detection of anti-donor antibodies and allows the simultaneous detection of antibodies against T-lymphocytes (anti-HLA class I antibodies) and B-lymphocytes (anti-HLA class I and/or HLA class II antibodies). Although the clinical relevance of a positive FCXM using T-lymphocytes in kidney graft outcome is well established, there is still debate about the clinical significance of a positive B-cell only FCXM (B+FCXM). In this review we discuss several factors to consider during the evaluation of patients with a B+FCXM and suggest ideas to improve the use of the information provided by the FCXM assay.