Somatic cells normally found in milk are generally either immune cells such as lymphocytes, monocytes and granulocytes, or mammary epithelial cells. The number and composition of somatic cells in milk can be influenced by a variety of factors, including infection and temperature-humidity index. The objective of this study was to determine the specific effects of heat stress on the cellular composition of the somatic cell population in milk. We used flow cytometry to ascertain the concentration and viability of mammary epithelial cells, T cells, monocyte/macrophage, and granulocytes in milk from cows maintained under heat stressed conditions compared to thermoneutral conditions. We found a significant 10% increase in the natural log concentration of epithelial cells in the milk of heat stressed cows compared to thermoneutral cows (9.3 vs. 8.4 ln(cells/mL, p = 0.02)). We also found a 12% decrease in the log concentration of live CD45+ cells (p = 0.04), and a 17% decrease in the log concentration of live CD45+ granulocytes (p = 0.04). No changes were found in CD3+CD45+ cells or CD14+CD45+ cells, however, we noted an unusual population of CD14+CD45− cells that showed significant increases of 10% (p = 0.03) and 12% (p = 0.01) in the log concentration of total and dead cells, respectively, under heat stressed conditions. These results suggest that heat stress influences the relative populations and viability of some somatic cells populations in milk. Increased losses of secretory epithelial cells into milk could have implications for milk production, and fewer viable immune cells could negatively impact the immunocompetence of dairy cows under heat stress.