This study was conducted to investigate the performance of a high-efficiency Heating, Ventilation and Air Conditioning (HVAC) filter and a top-of-the line Automotive Cabin Air (ACA) filter challenged with particles generated by the combustion of paper, wood, and plastic as well as with NaCl particles. The collection of submicron particles was examined under conditions representing two typical indoor air flow rates for the HVAC filter and two cabin fan control levels for the ACA filter. For the HVAC filter, almost all the collection efficiency values exceeded 80%; for the ACA filter, the collect efficiencies were much lower (< 40%) for all the tested aerosols and flow rates. Both filters demonstrated lower collection efficiency for combustion aerosols as compared to NaCl. This finding was consistent for all tested particle sizes and flow rates. The difference was always statistically significant in terms of the total efficiency (combining all sizes); however, the size-specific analysis of the differences revealed that the significance level varied with the particle size and flow rate. When tested under their operational flow conditions, the HVAC filter showed significantly better performance than the ACA filter. It was concluded that the filter performance characteristics of the HVAC and ACA filters obtained using well-established salt aerosol challenges may not accurately predict the performance of these filters against combustion aerosol particles. The difference was attributed to the interactions between the particles and filter fibers.