T cell development requires the interaction of developing thymocytes with thymic epithelial cells. Thymic epithelial cells acquire their unique phenotype under the control of the winged-helix transcription factor Whn, which is lacking in the nude mouse. Whn-dependent genes may therefore be important regulators of lympho-epithelial interactions. To identify Whn target genes we isolated RNA populations of wild-type and nude thymic anlagen from embryonic day 12.5 embryos by laser capture microdissection and compared them by gene expression profiling on microarrays representing 22,000 transcripts. All cDNA with expression differences confirmed by quantitative RT-PCR using RNA from individual anlagen and by in situ hybridization were found to be present in wild-type and absent in nude samples. Three of eight confirmed transcripts were of hematopoietic origin; these transcripts emanate from hematopoietic precursors which have just entered the thymic anlage. Five transcripts were of epithelial origin; one of these corresponds to the recently identified PD-1 ligand (PD-L1), the receptor of which is known to modulate positive selection and to play a role in the control of autoimmunity, and the remaining transcripts code for novel genes. The presented results support our prediction that this systematic approach by gene expression profiling yields regulators of thymopoiesis.