The application of a cell permeabilization technique to the analysis of nuclear import has led to many major breakthroughs in our understanding of this trafficking pathway. Digitonin permeabilization maintains the nucleus in a state competent for faithful, signal-dependent translocation through the nuclear pore complex. This system has also been used to probe the mechanism of hormone-regulated nuclear import through the use of glucocorticoid receptors (GR) as a model substrate. In this report we provide detailed descriptions of the digitonin-permeabilized cell system for use in studies of GR nuclear import. In addition, we present several novel applications that expand the utility of this system to probe for mechanisms of nuclear protein export and subnuclear trafficking. Copyright 1999 Academic Press.