The value of expression of epithelial–mesenchymal transition and cancer stem cell biomarker, glycogen synthase kinase 3ß (GSK3ß), and autophagy-related biomarkers, eukaryotic elongation factor 2 kinase (eEF2K) and autophagy- related 7 (Atg7), in triple-negative breast carcinomas (TNBCs) has not previously detected. Aim To detect the expression of GSK3ß, eEF2K, and Atg7 in breast cancer cells, particularly TNBCs, using immunohistochemistry, correlating their expression with each other, and with pathological and follow-up parameters to detect their prognostic role in such cancer. Materials and methods We have assessed the expression of GSK3ß, eEF2K, and Atg7 in tissues taken from 60 patients with TNBC using immunohistochemistry. We have followed patients for 3 years and detected associations between markers expression, clinicopathological findings, and follow-up data. Results High expression of GSK3ß and eEF2K and low expression of Atg7 were significantly associated with advanced stage of the tumor (P<0.001, P=0.002, and P<0.001, respectively), higher incidence of tumor recurrence (P=0.005, 0.006, and 0.029, respectively), and dismal outcome (P=0.002, 0.003, and 0.007, respectively). Conclusion We found that high expression of GSK3ß and eEF2K and low expression of Atg7 were related to progression of TNBC and dismal patient outcome.