Understanding forest stand structure is necessary for predicting losses and storage of carbon in forests. However, there is scanty knowledge on relationship between stand structure and carbon storage. This study assessed stand structure and its relationship with carbon storage in Nilo Nature Reserve. The specific objectives were to determine the forest stand structure, above ground and soil carbon stock and their relationship. The forest was stratified into four elevation bands. Four marked permanent sample plots of size 0.4 ha with 80 subplots of size 20 × 10 m one in each elevation band was established. In each plot, the following information was collected: tree diameter at breast height, wood cores, and soil samples. The data was used to determine species richness, stem density, basal area, volume and carbon stock. ANOVA was used to test variation in stand structure and carbon stock with elevation bands while regression analysis was used to determine their relationships. A total of 77 species of trees and shrubs belonging to 29 families were identified. Shannon index was 3.60 indicating high plant species diversity. The stand density, average diameter, basal area and volume were 299 ± 26 stems ha -1 , 26.07 ± 2.88 cm, 38.08 ± 3.61 m 2 ha -1 and 488.35 ± 56.32 m 3 ha -1 respectively. Above ground and soils carbon stocks were 291 ± 32.81 and 247.13 ± 73.38 t ha -1 respectively. There was significant correlation (P = 001) between carbon stocks and tree diameter, basal area and volume. Average diameter, basal area, volume and above ground carbon stock were significantly higher at high elevation than mid-high elevation band. It is concluded that stand structure correlated with carbon stocks and NNR has high potential for carbon storage in above ground biomass and soils. The stand structure parameters can be used adequately for prediction of carbon stock in similar forests.