A cardinal feature of protective T cell immunity is that activation induces a program of proliferation and differentiation resulting in the acquisition and long term maintenance of lineage-specific function. While it is known that the different functional capacities of naïve, effector and memory T cells are underscored by unique transcriptomes, how these arise and are maintained is poorly understood. We have previously demonstrated that differentiation-specific transcriptional signatures are established through modulation of histone post translational modifications (PTMS) and binding of activating and repressive transcription factors (TFs) to regulatory sequences including promoters and transcriptional enhancers (TEs)1, 2. However, how chromatin folding enables contact between gene promoters and targeted non-coding regulatory elements is not known. Genome wide mapping of chromatin interactions (HiC) and histone PTMs (ChIP-seq) demonstrated that while large scale higher order chromatin structures are stable across differentiation state, there were changes in genome contacts at a sub domain level at lineage specific gene loci. Interestingly, we identified that chromatin structures within killer T cells prior to infection (termed naive) exhibited a pre-configured structure, both at the level of histone PTMs and higher order chromatin contacts. This genomic pre-configuration was then associated with targeted epigenetic maturation of lineage-specific genomic elements upon T cell activation and acquisition of lineage-specific function, thus implying that the outcome of CD8+ T cell differentiation is largely pre-determined. These data have implications for the molecular events, and their regulation, that occur during the generation of effective T cell responses and establishment of immunological memory.