Peanut agglutinin, a lectin with high binding affinity for galactose-galactosamine disaccharide, was used to monitor changes in the photoreceptor cell layer of mice with inherited retinal degeneration. Mice homozygous for the retinal degeneration (rd) gene exhibit a rapid loss of rod photoreceptor cells in the first postnatal month. Previous studies have shown that aggregates of peanut agglutinin-binding cells are observed in the outer nuclear layer in the retinal degenerative mouse at between postnatal days 10 and 18, a period during which massive photoreceptor degeneration occurs in this mutant. This study was performed to determine whether these peanut agglutinin-positive cell clusters represent degenerating photoreceptor cells or, alternatively, macrophages that have migrated into the photoreceptor cell layer. Electron microscopic cytochemistry, using horseradish-peroxidase-conjugated peanut agglutinin, was used to trace cellular processes of peanut-agglutinin-stained cell clusters. Additionally, macrophage-specific antibodies were employed to determine whether macrophages were present in the clusters. The cell clusters did not react with macrophage-specific antibodies. However, processes of cells in peanut-agglutinin-bound clusters could be traced by electron microscopic serial sections to both the outer limiting membrane and the outer synaptic layer. These results provide strong evidence that peanut-agglutinin-bound cells seen during this stage of degeneration in the rd mouse are degenerating photoreceptor cells. Since peanut agglutinin has been shown to bind preferentially to cone, but not to rod, photoreceptor cells, the results also suggest that the clusters may be aggregates of degenerating cones.