Double labeling and color microradioautography were used in a new method of hybridization in situ to identify different genes in individual cells. The method is based on the unequal penetration of 3H and 35S into two layers of nuclear track emulsion separated by a thin barrier film. Hybridization of a 35S-labeled probe specific for one kind of gene results in silver grains over cells in both layers of emulsion; a 3H-labeled probe for a second gene provides grains only in the first layer of emulsion. Silver grains are converted to magenta-colored grains in the first layer and to cyan-colored grains in the second to facilitate enumeration of grains in each layer. This technique should be widely applicable in analyses of differential gene expression in single cells or in discrete populations of cells.