The association between organ volumes prior to allogeneic hematopoietic stem cell transplantation (allo-HSCT) and patient outcomes following the procedure remains unclear. Therefore, we evaluated the association between organ volumes-including of the kidneys, spleen, and liver-as evaluated via three-dimensional computed tomography (3D-CT), and outcomes following allo-HSCT. We retrospectively assessed data from 90 patients who underwent allo-HSCT for the first time at Yamaguchi University Hospital between 2016 and 2022. Organ volumes were adjusted to each patient's body surface area, and cutoff values were determined via receiver operating characteristic curve analyses for overall survival (OS). In our multivariate analyses, kidney volume (KV) of ≥ 198 mL/m and spleen volume (SV) of < 60 mL/m represented independent risk factors for worse OS (hazard ratio [HR]: 2.80, 95% confidence interval [CI]: 1.27-6.14; and HR: 2.06, 95% CI: 1.14-3.70, respectively), while a KV of ≥ 198 mL/m was an independent risk factor for non-relapse mortality (HR: 16.93, 95% CI: 3.88-73.91). The incidence of sinusoidal obstruction syndrome was also higher in the patients with KVs of ≥ 198 mL/m vs. those that were < 198 mL/m (10.5% vs. 0.0%, P < 0.01). We found that large KVs and small SVs, but not liver volumes as measured via 3D-CT, correlated with worse outcomes following allo-HSCT.