Delivery of nano-objects to specific cellular sub-domains is a challenging but intriguing task. There are two major barriers on the way of a nano-object to its intracellular target: (1) the cell membrane and (2) the intracellular barriers. The former is a common issue for all nanomedicine and a matter of very intense research. The latter is the primary problem for targeted delivery of nano-objects to specific cellular sub-domains and can be studied more easily using permeabilized cells. Membrane permeabilization for nanomedical research requires (1) perforation of the outer membrane, (2) development of a solution that will keep cellular sub-domains in the functional state, and (3) modification of the perimembrane cytoskeleton. We developed a very successful model of saponin membrane permeabilization of cardiomyocytes. This allowed us to deliver particles up to 20 nm in size to perinuclear and perimitochondrial space. Here we describe the method.