Retail stores contain a wide range of products that can emit a variety of indoor pollutants. Among these chemicals, phthalate esters and polybrominated diphenyl ethers (PBDEs) are two important categories of semi-volatile organic compounds (SVOCs). Filters in heating, ventilation, and air-conditioning (HVAC) system collect particles from large volumes of air and thus potentially provide spatially and temporally integrated SVOC concentrations. This study measured six phthalate and 14 PBDE compounds in HVAC filter dust in 14 retail stores in Texas and Pennsylvania, United States. Phthalates and PBDEs were widely found in the HVAC filter dust in retail environment, indicating that they are ubiquitous indoor pollutants. The potential co-occurrence of phthalates and PBDEs was not strong, suggesting that their indoor sources are diverse. The levels of phthalates and PBDEs measured in HVAC filter dust are comparable to concentrations found in previous investigations of settled dust in residential buildings. Significant correlations between indoor air and filter dust concentrations were found for diethyl phthalate, di-n-butyl phthalate, and benzyl butyl phthalate. Reasonable agreement between measurements and an equilibrium model to describe SVOC partitioning between dust and gas-phase is achieved.