The goal of our study was to evaluate at the systems-level, the effect of sex hormones on thymic epithelial cells (TECs). To this end, we sequenced the transcriptome of cortical and medullary TECs (cTECs and mTECs) from three groups of 6 month-old mice: males, females and males castrated at four weeks of age. In parallel, we analyzed variations in the size of TEC subsets in those three groups between 1 and 12 months of age. We report that sex hormones have pervasive effects on the transcriptome of TECs. These effects were exquisitely TEC-subset specific. Sexual dimorphism was particularly conspicuous in cTECs. Male cTECs displayed low proliferation rates that correlated with low expression of Foxn1 and its main targets. Furthermore, male cTECs expressed relatively low levels of genes instrumental in thymocyte expansion (e.g., Dll4) and positive selection (Psmb11 and Ctsl). Nevertheless, cTECs were more abundant in males than females. Accumulation of cTECs in males correlated with differential expression of genes regulating cell survival in cTECs and cell differentiation in mTECs. The sexual dimorphism of TECs highlighted here may be mechanistically linked to the well-recognized sex differences in susceptibility to infections and autoimmune diseases.The immune system of vertebrates shows a major sexual dimorphism. Thus, relative to males, females usually display stronger immune response to vaccination and infection but suffer a higher propensity to many autoimmune diseases 1-4 . Though we have limited insight into the mechanistic bases for these differences 4 , evidence suggests that they result from both direct and indirect effects of sex steroids on innate and adaptive immune responses. Thus, sex hormones can affect immune cells directly or via modulation of the gut microbiome which in turn influences the immune response 5-9 . Sex-based differences in thymus biology have been observed in many studies. Thymic involution, which affects all vertebrates 10,11 , accelerates at puberty and progresses at different rates in males and females [12][13][14] . Also, administration and ablation of androgens respectively accelerates and reverses, albeit transiently, thymic involution [15][16][17][18][19] . Nevertheless, it remains unclear to what degree sex steroids' impact on thymic cellularity may reflect the influence of hormones on thymic epithelial cells (TECs) 3 vs. other cell types (thymocytes, mesenchymal cells).Recent studies have shown that sex steroids do affect TECs. In adult mice, cortical and medullary TECs (cTECs and mTECs) have slower proliferation rates in males than females 20 . Furthermore, following acute ablation in a transgenic mouse model, cTECs were found to regenerate in females and castrated (Cx) males, but not in males or androgen-treated females 21 . Finally, it was recently shown that, in TECs, androgens repress transcription of the Notch ligand Dll4 22 which is essential for specification, commitment, and development of thymocytes 23 . Nevertheless, studies in other cell types (e.g., liver, adip...