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Background: Many studies evaluated the role of paired box gene 5 (PAX5) in breast cancer. However, few investigated PAX5α and PAX5β isoforms individually. Objective: The aim of the present study is to evaluate mRNA expression of PAX5α and PAX5β in breast cancer and assessing their underlying pathological roles through investigating their correlations to matrix metalloproteinase2 (MMP2), p53 and cancer antigen 15-3 (CA15-3). Methods: Evaluation of PAX5α and PAX5β RNA expression in breast tissue samples was done by real-time PCR, serum MMP2 and p53 by ELISA and CA15-3 by chemiluminescent immunoassay in 55 infiltrating ductal carcinoma patients, 25 fibroadenoma patients and 15 control females who underwent plastic breast surgery. Results: PAX5α RNA was reduced while PAX5b RNA was elevated in breast cancer patients compared to other groups (p < 0.01). The best cutoff value of PAX5α was 61.15 with 78.2% sensitivity and 90% specificity and for PAX5β it was P2.01 with 83.6% sensitivity and 82.5% specificity. The RNA expression of PAX5β was higher in advanced grades and stages (p < 0.01), and significantly correlated to p53 (r: 0.51, p < 0.01), and CA15-3 (r: 0.45, p < 0.01). Moreover, PAX5α was negatively correlated to PAX5β (r: 0.42, p < 0.01), p53 (r: 0.53, p < 0.01) and MMP2 (r: 0.22, p < 0.05). Conclusions: The downregulation of PAX5α with upregulation of PAX5β RNA expressions could highlight the possible oncogenic role of PAX5 as a transcriptional factor in tumorigenesis and progression of breast cancer.