T cell receptor (TCR) α alleles undergo primary and secondary rearrangement in double-positive (DP) thymocytes. By analyzing TCRα rearrangement in orphan nuclear receptor RORγ-deficient mice, in which the DP lifespan is shorter, and in Bcl-x_L–transgenic mice, in which the DP lifespan is extended, we show that the progression of secondary V_α to J_α rearrangements is controlled by DP thymocyte survival. In addition, because Bcl-x_L induces a bias towards 3′ J_α usage in peripheral T cells, we conclude that the programmed cell death of DP thymocytes is not simply a consequence of failed positive selection. Rather, it limits the progression of rearrangement along the J_α locus and the opportunities for positive selection, thereby regulating the TCRα repertoire.