The Hedgehog (Hh) signalling pathway influences multiple stages of murine T-cell development. Hh signalling mediates transcriptional changes by the activity of the Gli family of transcription factors, Gli1, Gli2 and Gli3.  Both Gli2 and Gli3 are essential for mouse development and can be processed to function as transcriptional repressors or transcriptional activators, whereas Gli1, itself a transcriptional target of Hh pathway activation, can only function as a transcriptional activator and is not essential for mouse development.  Gli1-deficient mice are healthy and appear normal and non-redundant functions for Gli1 have been difficult to identify.  Here we show that Gli1 is non-redundant in the regulation of T-cell development in the thymus, at multiple developmental stages.  Analysis of Gli1-deficient embryonic mouse thymus shows a role for Gli1 to promote the differentiation of CD4-CD8- double negative (DN) thymocytes before pre-TCR signal transduction, and a negative regulatory function after pre-TCR signalling.  In addition, introduction of a Class I-restricted transgenic TCR into the adult Gli1-deficient and embryonic Gli2-deficient thymus showed that both Gli1 and Gli2 influence its selection to the CD8 lineage.