Little is known about the histologic features of a latent Monilinia fructicola infection and brown rot in infected fruit. This report informs on the results of an investigation whose aim was to analyze the microanatomy of nectarines with a latent and visible M. fructicola infection. Mature nectarines were inoculated with an M. fructicola isolate and incubated at 25°C for 0, 24, 48, 72, or 96 hours in the dark. For investigating the latent infection process, the inoculated nectarines were first incubated at 25°C for 24 hours in the dark and then incubated at 4°C for 72, 144, 216, and 288 hours in the dark. At the end of the incubation, samples of nectarine tissue were excised from the inoculation points and prepared for light and transmission electron microscopic examinations. No signs of disease were seen on the surface of nectarines with a latent infection over the 288-hour incubation period. When the tissue samples were microscopically examined, M. fructicola colonized the stomata and this stomatal colonization progressively increased over time and was associated with gradual collapse of the epidermal cells and colonization of the subepidermis. In nectarines with visible brown rot, the disease usually appeared after 24 hours on the surface and in the uppermost layers of epidermal cells, which began to collapse after 48 hours. Subsequently, the diseased tissues of the nectarines displayed (a) colonization of the epidermis and mesocarp by M. fructicola with thin and thick hyphae, (b) collapse and disruption of epidermal and mesocarpic cells, (c) lysogenic cavities in the subepidermis and mesocarp, (d) degradation of the cuticle and epidermis, and (e) M. fructicola sporulation. M. fructicola is active during latent infections because slow and progressive colonization of nectarine subcuticular cells by the fungus occurs.