The Third International Conference on Regulatory T cells and Th Subsets and Clinical Application in Human Diseases was held in Shanghai, China during 13–15 October 2012. This conference, organized by Shuiping Jiang, the Conference Founder and President, and Xuetao Cao, the President of Chinese Society for Immunology, brought together many prominent experts in the field of regulatory T cells (Tregs) and T helper cells (Th) subsets immunology and highlighted the cutting-edge advancements on the development, function, homeostasis and interplay of Tregs and Th subsets, especially the latest breakthrough in therapeutic applications in clinical settings.