This study investigates the congener-specific concentrations of polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs), polybrominated dibenzo-p-dioxins/furans (PBDD/Fs), and polybrominated diphenyl ethers (PBDEs) in 25 breast milk samples from southern Taiwan. Most investigated congeners in Taiwanese breast milk are detectable except for PBDD/Fs. The geometric means of PCDD/Fs and PBDEs in the breast milk are 2.44 pg WHO-TEQ/g lipid and 2810 pg/g lipid. Several PCDD/F and PBDE congeners were highly correlated to each other like 1,2,3,7,8-PeCDD and 2,3,4,7,8-PeCDF (r = 0.919, p < 0.001). The longest duration of menstruation could be predicted by BDE-153 (β = 0.252) and 1,2,3,4,6,7,8-HpCDF (β = 0.345) with adjustment of confounders using a multiple stepwise linear regression model (r = 0.963, p < 0.001).