The buoyant density of intracellular organelles is dependent in part on the nature of the buffer composition of the density gradient and the permeability characteristics of the organelle membrane to the constituents of this buffer. Therefore, knowledge of the transport properties of different organelles allows the design of density gradients useful for their purification. We have used this approach to significantly decrease mitochondrial contamination of pancreatic zymogen granules in a one-step purification procedure on a 40% Percoll density gradient. These gradients, prepared with isoosmotic sucrose, yield a narrow band of zymogen granules and mitochondria. However, by substitution of sucrose with salts to which mitochondria but not zymogen granules are permeable, the densities of mitochondria are altered to give a significant separation. For example, the incorporation of 100 mM sodium succinate in the Percoll gradient can produce a 70% reduction in mitochondrial contamination. The increased ionic strength has an additional beneficial effect on zymogen granule yield by 5-10%. The recognition and utilization of transport pathways in organelle membranes is the principal feature of this technique and should prove to be widely applicable to other isolation procedures.