The cell is the basic unit of life. The acquisition of a nucleus to house the genetic material is thought to have provided a distinct advantage to the evolving cell, ultimately allowing the emergence of differentiated, specialized cells. Whereas much effort over the last five decades has been devoted to understanding the genetic material by biochemical approaches and sequencing, our understanding of how these materials are stored physically is only just emerging. Accumulating evidence suggest that genomes are organized non-randomly into complex 3D configurations that vary according to cell type, stage of development, differentiation and disease status. The principles, which guide higher order organization, the mechanisms responsible for establishment, maintenance and alterations of higher order genome, and the functional consequences of aberrant genome and nuclear organization have become areas of intense interest. The higher-order spatial and temporal organization of genomes in the cell nucleus is rapidly emerging as a driver of biological function in differentiation, development and disease and the incorporation of information on higher order genome organization add an additional level of complexity in our understanding of genome regulation. These studies bring together several cutting edge fields including genomics, epigenetics, big data analysis, imaging and clinical cell and molecular biology. The 2015 conference on Genome Architecture in Cell Fate and Disease aims to foster a new community that is devoted to the understanding of nuclear architecture in cell fate determination, development, disease modeling, stem cell biology and regenerative medicine. Particularly emphasis will be placed on genome organization, epigenetic remodeling, chromatin folding, and structural elements of the nucleus. Another angle is to promote cutting edge tools that allow us to visualize the nucleus. We seek to unify and integrate chemical, biological, physiological as well as physical parameters into a coherent picture of the nucleus, especially the human one.