Probability models incorporating a deterministic versus stochastic infectious dose are described for estimating infection risk due to airborne pathogens that infect at low doses. Such pathogens can be occupational hazards or candidate agents for bioterrorism. Inputs include parameters for the infectious dose model, distribution parameters for ambient pathogen concentrations, the breathing rate, the duration of an exposure period, the anticipated number of exposure periods, and, if a respirator device is used, distribution parameters for respirator penetration values. Application of the models is illustrated with a hypothetical scenario involving exposure to Coccidioides immitis, a fungus present in soil in areas of the southwestern United States. Inhaling C. immitis spores causes a respiratory tract infection and is a recognized occupational hazard in jobs involving soil dust exposure in endemic areas. An uncertainty analysis is applied to risk estimation in the context of selecting respiratory protection with a desired degree of efficacy.