The two aims of this study were (i) to compare the effects of prolonged exercise on circulating neutrophil number and muscle myeloperoxidase (MPO) activity between RAG2/gamma c null and immune-competent mice, and (ii) to evaluate the general suitability of the lymphocyte-deficient RAG2/gamma c null strain for use in exercise models of immune regulation. RAG2/gamma c null (male and female) and C57BL/6 (congenic immune-competent, male) mice were assigned to either control (C) or treadmill exercise (EX, 22 m/min, 90 min, 6% grade) groups. EX mice were killed immediately (EX0) or 24 h (EX24) after exercise. RAG2/gamma c null males had significantly (P < 0.05) fewer circulating CD45+ cells and higher %CD45+ neutrophils than did C57BL/6 males, independent of exercise. A significant interaction was observed for the effects of exercise and gender on %CD45+ neutrophils in the blood. At EX24, gastrocnemius (Gastroc) MPO significantly increased in EX mice. Gastroc MPO activity was 44% and 35% higher in RAG2/gamma c null vs. C57BL/6 males, and in female vs. male RAG2/gamma c null mice, respectively. Heart MPO activity did not differ between strains or among treatments. We concluded that the Rag2/gamma c null strain is a suitable model for future investigations on immune regulation following acute exercise stress.