Polybrominated diphenyl ether (PBDE) flame retardants (FRs) have been ubiquitously detected at high concentrations in indoor environments; however, with their recent phase-out, more attention is being focused on measurements of exposure to alternative FRs such as organophosphate FRs (OPFRs). In our previous research, we found that PBDE residues measured on children’s handwipes were a strong predictor of serum PBDE levels. Here we build upon this research to examine longitudinal changes in PBDEs in indoor dust and children’s handwipes, and explore the associations between handwipes and dust for alternative FRs. Children from our previous study were re-contacted after approximately two years and new samples of indoor dust and handwipes were collected. PBDE dust-levels were significantly correlated between two different sampling rounds separated by two years; however, PBDE levels in handwipes were not correlated, perhaps suggesting that the sources of PBDEs remained relatively constant in the home, but that behavioral differences in children are changing with age and influencing handwipe levels. OPFRs [i.e. tris (1,3-dichloroisopropyl) phosphate (TDCPP), tris(2-chloroethyl) phosphate (TCEP), tris(2-chloroisopropyl) phosphate (TCIPP)], 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (EH-TBB, also known as TBB), di(2-ethylhexyl) tetrabromophthalate (BEH-TEBP, also known as TBPH), and 1,2,5,6,9,10-hexabromocyclododecane (HBCD) were also ubiquitously detected in house dust samples and geometric mean levels were similar to PBDE levels, or higher in the case of the OPFRs. Significant associations between handwipes and house dust were observed for these alternative FRs, particularly for EH-TBB (rs= 0.54; p<0.001). Increasing house dust levels and age were associated with higher levels of FRs in handwipes, and high hand washing frequency (>5 times/day) was associated with lower FR levels in handwipes. Overall these data suggest that exposure to these alternative FRs will be similar to PBDE exposure, and the influence of hand-to-mouth behavior in children’s exposure needs to be further examined to better estimate exposure potential.