While mutations in human FOXP3 predispose individuals to autoimmune conditions, it is unclear how the mutant protein fails to function as a transcriptional regulator. There is also limited detail of how FOXP3 itself interacts with the transcriptional machinery and which components of the FOXP3 ensembles exert phenotypic changes to render cells able to mediate suppression. Increasing evidence indicates that the level and duration of FOXP3 expression plays a crucial role in the development and function of natural regulatory T cells (Tregs). Our studies focus on the post-translational modification of the FOXP3 protein, and how the FOXP3 complex ensemble, containing histone modification and chromatin-remodeling enzymes, defines its functional role in regulatory T cells. Understanding the molecular mechanisms underlying FOXP3 activity will provide therapeutic implications for transplantation, allergy, autoimmune disease and cancer.