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Allometric equations are routinely used in the estimation of biomass stocks for carbon accounting within forest ecosystems. However, generic equations may not reflect the growth trajectories of afforestation species that are introduced to degraded farmland characterized by water and nutrient limitations. Using sequential measurements of the height, basal diameter, and above- and belowground biomass of juvenile trees, we developed allometric equations for five woody species (Moringa oleifera Lam., Leucaena leucocephala Lam., Jatropha curcas L., Anacardium occidentale L. and Parkia biglobosa Jacq.) subjected to a gradient of water and nutrient availability in an afforestation trial on degraded cropland in the semi-arid zone of Benin, West Africa. For three of the species studied, the allometric relationships between basal diameter and biomass components (i.e. leaves, stems and roots) were described best by a simple power-law model (R-2 > 0.93). The incorporation of species-specific height-diameter relationships and total height as additional predictors in the power-law function also produced reasonable estimates of biomass. Fifteen months after planting, roots accounted for 10-58% of the total biomass while the root-to-shoot ratio ranged between 0.16 and 0.73. The total biomass of the saplings ranged between 1.4 and 10.3 Mg ha(-1), yielding 0.6-4.3 Mg C ha(-1), far exceeding the biomass in the traditional fallow system. The rate of stem carbon sequestration measured ca. 0.62 Mg C ha(-1) year(-1). Overall, the allometric equations developed in this study are generally useful for assessing the standing shoot and root biomass of the five afforestation species during the juvenile growth stage and can help in reporting and verifying carbon stocks in young forests.