The performance of three filtering facepiece respirators (two models of N99 and one N95) challenged with an inert aerosol (NaCl) and three virus aerosols (enterobacteriophages MS2 and T4 and Bacillus subtilis phage)—all with significant ultrafine components—was examined using a manikin-based protocol with respirators sealed on manikins. Three inhalation flow rates, 30, 85, and 150 l min−1, were tested. The filter penetration and the quality factor were determined. Between-respirator and within-respirator comparisons of penetration values were performed. At the most penetrating particle size (MPPS), >3% of MS2 virions penetrated through filters of both N99 models at an inhalation flow rate of 85 l min−1. Inhalation airflow had a significant effect upon particle penetration through the tested respirator filters. The filter quality factor was found suitable for making relative performance comparisons. The MPPS for challenge aerosols was <0.1 μm in electrical mobility diameter for all tested respirators. Mean particle penetration (by count) was significantly increased when the size fraction of <0.1 μm was included as compared to particles >0.1 μm. The filtration performance of the N95 respirator approached that of the two models of N99 over the range of particle sizes tested (∼0.02 to 0.5 μm). Filter penetration of the tested biological aerosols did not exceed that of inert NaCl aerosol. The results suggest that inert NaCl aerosols may generally be appropriate for modeling filter penetration of similarly sized virions.