The rare memory B-cells in thymus are considered the cell of origin for primary mediastinal large B-cell lymphoma (PMBL). The goals for the present study were to characterize the normal memory B-cell compartment in thymus and support its association to primary mediastinal B-cell lymphoma. Seven paired human tissue samples from thymus and sternum bone marrow were harvested during cardiac surgery. B-cell subsets were phenotyped by Euroflow standard and FACS-sorted for microarray analysis on the Human Exon 1.0 ST Arrays platform. Differentially expressed genes between thymus and bone marrow memory B-cells were identified and correlated to the molecular subclasses of diffuse large B-cell lymphoma. Within thymus, 4% (median, range 2-14%) of the CD45(+) haematopoietic cells were CD19(+) B-cells with a major fraction being CD27(+)/CD38(-) memory B-cells (median 80%, range 76-93%). The bone marrow contained 14% (median, range 3-27%) of which only a minor fraction (median 5%, range 2-10%) was memory B-cells. Global gene expression analysis of the memory B-cell subsets from the two compartments identified 133 genes up-regulated in thymus, including AICDA, REL, STAT1, TNF family, SLAMF1, CD80 and CD86. In addition, Exon 4 and 5 in the 3`end of AICDA was significantly higher expressed in thymus compared to bone marrow. The thymus memory B-cell gene profile was over-expressed in primary mediastinal B-cell lymphoma when compared to other DLBCL subclasses. The present study describes a thymus memory B-cell subset and its gene profile correlated to primary mediastinal B-cell lymphomas, supporting that it may arise from thymus memory B-cells.