A new university hospital was designed to maximize the air quality protection of severely compromised patients undergoing transplantation or treatment for malignant disorders. The entire hospital was designed as a sealed building with two filter systems having >95% efficiencies for 1.0 μm particles. Controlled airflow and isolation of the most severely compromised patients were also design features. Air quality monitoring of particles and airborne fungi demonstrate effective control in the patient environment. The results show the areas with the greatest control of personnel and air changes have the lowest airborne concentrations of fungi and the smallest particles. Larger indoor airborne particle ranking indicate highest levels depending on local human activity, air change rates, or filtration efficiency.