Due to the complexity and redundancy of molecular processes governing the development and function of haematopoietic cells, experimental procedures allowing simultaneous alteration in gene expression of multiple genes in vivo are needed. Here, we describe a protocol allowing for simultaneous transduction of haematopoietic stem cells (HSC) with two different replication incompetent retroviral expression vectors followed by transplantation of lethally irradiated recipient mice. These bicistronic retroviral vectors carried genes for the enhanced green and yellow florescent proteins (EGFP and EYFP) respectively. Spleen cells from reconstituted animals were stained for common lymphocyte and myeloid markers, then analysed on a two-laser, 488 and 635 nm, flow cytometer equipped with a 510/20-nm bandpass filter for FL1, a 550/30-nm bandpass filter for FL2 and a 530-nm short-pass dichroic mirror. It was demonstrated that cells expressing EGFP, EYFP or combinations thereof could be distinguished and analysed for staining with PerCP- and APC-conjugated reagents. We found that a sizable proportion of cells (70%) from reconstituted animals expressed EGFP and/or EYFP and that expression of these genes did not affect lymphoid or myeloid development. We also demonstrated that the alternative optical configuration allowed for conventional multiparameter flow cytometric analyses.