Cynomolgus macaques (CYNO; Macaca fascicularis) are a well-established NHP model used for studies in immunology. To provide reference values on the baseline cell distributions in the hematopoietic and lymphoid organs (HLO) of these animals, we used flow cytometry to analyze the peripheral blood, bone marrow, mesenteric lymph nodes, spleen, and thymus of a cohort of male, adult, research-naïve, Mauritian CYNO. Our findings demonstrate that several cell distribution patterns differ between CYNO and humans. First, the CD4(+):CD8(+) T-cell ratio is lower in CYNO compared with humans. Second, the peripheral blood of CYNO contains a population of CD4(+)CD8(+) T cells. Third, the CD31 level was elevated in all organs studied, suggesting that CD31 may not be an accurate marker of recent thymic emigrants within the CD4(+) T cells of CYNO. Finally the B-cell population is lower in CYNO compared with humans. In summary, although the majority of immune cell populations are similar between cynomolgus macaques and humans, several important differences should be considered when using CYNO in immunologic studies. Our current findings provide valuable information to not only researchers but also veterinarians working with CYNO at research centers, in zoos, or in the wild.