The development of T cells in the thymus involves several differentiation and proliferation events, during which hematopoietic precursors give rise to T cells ready to respond to antigen stimulation and undergo effector differentiation. This review addresses signaling and transcriptional checkpoints that control the intrathymic journey of T cell precursors. We focus on the divergence of αβ and γδ lineage cells and the elaboration of the αβ T cell repertoire, with special emphasis on the emergence of transcriptional programs that direct lineage decisions.