Polybrominated diphenyl ethers (PBDEs) have been used as flame retardants. Although many reports have indicated an association between exposure to PBDEs and developmental neurotoxicity, the relative contributions of different sources of dust PBDE congeners to the levels in various tissues of mother–baby pairs is not well understood. The aims of this study were thus to measure the quantitative relationship between the level of PBDEs in house dust and tissues of mother-neonate pairs, and to investigate the chemical sources of the PBDEs. Forty-one mother-neonate pairs were recruited and provided samples of maternal serum (n = 29), umbilical cord serum (n = 25), breast milk (n = 50), and house dust (n = 41), where PBDEs were determined with high-resolution gas chromatography coupled with high-resolution mass spectrometry. While deca- (e.g., BDE 209, detected 100%), nona- (BDE 206/207, 95.1%), octa- (BDE 183, 100%), penta- (BDE 99/153, 100%, 98%) and tetra-BDEs (BDE 47, 100%) were detected abundantly in dust, penta- (BDE 99, 76%, 92%) and tetra-BDEs (BDE 47, 84%, 98%) were detected abundantly in umbilical cord serum and breast milk, respectively; tetra-BDEs (BDE 47, 86%) were detected more often relative to other congeners in maternal serum. Spearman’s pairwise comparison showed that the levels of BDE 47 (ρ = 0.52, p < 0.001) and −99 (ρ = 0.64, p < 0.01) in umbilical cord serum were associated with BDE 209 levels in dust; BDE 47 in maternal serum also showed correlation with BDE 99 in cord serum (ρ = 0.48, p < 0.01) but there was no significant correlation between maternal BDE 47 and dust BDE 209. On the other hand, a comparison of the distribution among congeners suggested probable associations of BDE 47 in maternal serum, breast milk, and umbilical cord serum with BDE 209 in dust; and of BDE 99 in maternal and umbilical cord serum, breast milk, and dust with BDE 209 in dust. Although further studies are needed, a radar chart-based distributional comparison among congeners supported associations between BDE 47 or −99 in human tissues and BDE 209 in dust.