Background: Aldehyde dehydrogenase 1 (ALDH1) is an enzyme accountable for the detoxification of aldehydes. Sex-determining region Y-box 9 (SOX-9) plays a role in many biological and pathological processes. In this study, we aimed to evaluate the prognostic significance of ALDH1 and SOX9 expression in early breast cancer. Method: The expression of ALDH1 and SOX-9 was evaluated through immunohistochemistry derived from 50 eligible patients with early breast cancer included in the current prospective cohort study. Results: Positive expression of ALDH1 and SOX-9 were detected in 29 (58%) and 34 (68%) patients, respectively. The positive expressions of both markers were statistically significant associated with increasing the stage, lymph nodes metastasis, high Ki67 labeling index, and molecular subtypes (P < 0.001), along with with the biological markers; estrogen receptors, progesterone receptors, and human epidermal growth factor receptor 2 over-expressions, and large tumor size (P = 0.039, P = 0.022, P = 0.024 and P = 0.003 for ALDH1 expression and P = 0.012, P = 0.007, P = 0.004 , and P = 0.002 for SOX-9 expression, respectively). There is a significant positive association between the expression of ALDH1 and SOX-9, r (correlation coefficient) = +0.806 (P < 0.001). Local recurrence was associated with the positive expression of ALDH1 only (P = 0.045) and the disease progression was statistically significant and associated with the positive expression of both ALDH1 and SOX-9 (P = 0.038, P = 0.023, respectively). There was significant association of positive expression of SOX-9 with reduced 3-y disease-free survival (P = 0.039). Conclusion: Positive expression of ALDH-1 and SOX9 were associated with aggressive histopathological features and poor outcome in early breast cancer and can be considered potential prognostic markers in this group of patients.