Inert particles are widely used as surrogates for biological particles in filtration tests. However, there is always a concern that the different physical properties between inert particles and biological particles may affect the filtration efficiencies of filter media. In the present study, the inert particles, e.g. NaCl and polystyrene latex (PSL), and biological particles, e.g. E.coli, B.sublitis, bovine serum albumin (BSA), and endotoxin, were used to evaluate the filtration efficiencies of the filtering materials of a surgical mask and a N95-rated respirator. The results showed that the difference in the filtration efficiencies of the N95-rated respirator for the tested inert particles and biological particles was smaller than 0.02%. The filtration efficiency of the surgical mask for PSL particles was lower than that for E.coli and B.subtilis particles with the same aerodynamic diameter because of the larger interception lengths of E.coli and B.subtilis particles. The average filtration efficiencies of the surgical mask for the tested NaCl particles and biological particles in the size range of 20–600 nm were similar. For the monodisperse particles, the filtration efficiency of the surgical mask for NaCl, BSA and endotoxin particles in the size range of 50–250 nm decreased in the above order due to the different shapes, dielectric properties, and multiply-charged fractions of the particles. The surgical mask presented the highest filtration efficiency for BSA particles and the lowest filtration efficiency for NaCl particles when the particle size was larger than 300 nm, which could be related to the difference in the electrostatic deposition and bounce probabilities. The present work revealed that the influence of several particle characteristics such as shape, dielectric property, and charge state on filtration efficiency should be considered when using common inert particles to replace biological particles to measure efficiencies of air filters.