We examined age and nutritional related changes in the distribution and size of gut associated lymphoid tissues in the intestinal tract of cotton rats (Sigmodon hispidus). Peyer's patches in the small intestine are prominent, ranging from four to 13, and increase in size (surface area) with age. The average Peyer's patch in the adult cotton rat measured 23.9 mm². Lymphoid tissue in the cecum was primarily limited to a large aggregate located in the vermiform appendix, which increased in size with age. Age related changes in the number of visible lymphoid follicles in the large intestine were highly significant, increasing from 24.8 in juveniles to 45.1 in adults. Weights of dissectable Peyer's patch tissue in animals consuming a low protein diet were significantly lower in juveniles and greater in subadults compared to those on high protein diets. Relative weights of Peyer's patch tissue averaged 84 to 95% more in low protein-fed animals than in the group on the high quality protein diet. Our results suggest that peripheral lymphoid tissues in wild cotton rats are more resistant to protein deficiencies than other tissues in the body and could be a useful index for assessing nutritional status.