This study aimed to investigate the diagnostic value of miR-451a, miR-5571-3p, CLN6, HSD11B1, and PDE4 as potential biomarkers for distinguishing patients with Granulomatous lobular mastitis (GLM), breast cancer (BC), and breast fibroadenoma. A total of 55 participants were included in each group. The serum expressions of miR-451a and miR-5571-3p were significantly higher in the GLM (0.95 ± 0.47, 7.20 ± 3.99) and control groups (0.21 ± 0.13, 1.74 ± 1.49) than in the BC group (p < 0.01). Meanwhile, the expression of miR-451a and miR-5571-3p in GLM was significantly higher than in the control group (0.21 ± 0.13, 1.74 ± 1.49; p < 0.001). The levels of CLN6 in the GLM(1.37 ± 0.87) and BC((1.57 ± 0.84) groups were higher than those in the control group (p < 0.001). Furthermore, HSD11B1 and PDE4 expressions were significantly increased in the BC (1.92 ± 1.14, 1.54 ± 0.88) and GLM (1.07 ± 0.70, 0.85 ± 0.51) groups compared to the control group (p < 0.01), with higher levels observed in the BC group than in the GLM group (p < 0.01). Taken together, these findings suggest that serum miR-451a, miR-5571-3p, and CLN6 may serve as noninvasive biomarkers for differentiating GLM, BC, and breast fibroadenoma. This study provides a basis for future investigations in the differential diagnosis of these breast diseases.