The mRNA expression of essential genes involved in B cell differentiation was tested in bone marrow samples of horses with CVID (1 to 8) and control healthy horses (A, B, C). Standard RT-PCR revealed that all equine CVID patients expressed RUNX1, PU.1, IRF8, CD43, FLT3LG, IL7R, IL7, B220, and EBF1, which are transcription factors and key signaling molecules that directly regulate B cell differentiation up to PAX5 expression. Yet, the expression of E2A, PAX5 and its target genes CD79A, BLK, BLNK, IGKC CD19 and IGHM was variable, with some patients missing the expression of those genes in their bone marrow.