Species of Perkinsus are responsible for high mortalities of bivalve molluscs world-wide. Techniques to accurately estimate parasites in tissues are required to improve understanding of perkinsosis. This study quantifies the number and tissue distribution of Perkinsus marinus in Crassostrea virginica by modern stereology and immunohistochemistry. Mean total number of trophozoites were (mean ± SE) 11.80 ± 3.91 million and 11.55 ± 3.88 million for the optical disector and optical fractionator methods, respectively. The mean empirical error between both stereological approaches was 3.8 ± 1.0%. Trophozoites were detected intracellularly in the following tissues: intestine (30.1%), Leydig tissue (21.3%), hemocytes (14.9%), digestive gland (11.4%), gills (6.1%), connective tissues (5.7%), gonads (4.1%), palps (2.2%), muscle (1.9%), mantle connective (0.8%), pericardium (0.7%), mantle epithelium (0.1%), and heart (0.1%). The remaining 0.6% were found extracellularly. Percentages of trophozoite stages were (mean ± SE): large, log-phase trophonts, i.e., signet rings, 97.0 ± 1.2%; meronts, 2.0 ± 0.9%; clusters of small, log-phase trophonts, i.e., merozoites, 1.0 ± 0.5%. Levels of infection in hemocytes and Leydig tissue were representative of total parasite intensity. These techniques are a powerful tool to follow parasite distribution and invasion, and to further explore mechanisms of Perkinsus spp. pathogenesis in bivalves.