Toll-like receptor 9 (TLR9) recognizes microbial and vertebrate DNA. We previously demonstrated TLR9 expression in human breast cancer cell lines and showed that TLR9 ligands stimulate their in vitro invasion. The aim of this study was to characterize TLR9 expression in clinical breast cancer specimens. Immunohistochemical staining intensity was compared with known baseline prognostic factors and distant metastasis-free survival. TLR9 expression was detected in 98% of the tumors studied (n = 141). The mean TLR9 staining intensity was higher in ER- than in the highly ER+ breast cancers (p = 0.039). High-grade tumors had significantly increased TLR9 expression (p = 0.027) compared with lower-grade tumors. The highest TLR9 expression was detected in the mucinous and the lowest in the tubular breast cancers (p = 0.034). Distant metastasis-free survival was higher in the lower TLR9-expressing half of the cohort than in the higher TLR9-expressing group (p = 0.118). TLR9 expression did not correlate with menopausal, PgR or Her2 status, patient age, tumor proliferative or invasive characteristics.