Hygienic design of the Air Handling Unit (AHU), the custom-designed industrial HVAC system used in hospitals, laboratories, and similar sterile areas to supply clean, filtered, and conditioned air, has become more prevalent during the covid-19 pandemic. Improper maintenance of the air handling system can carry germs or viruses at any stage. This study concentrates explicitly on Air Handling Units used in hospitals, which should maintain higher quality standards than conventional air handling systems to reduce all kinds of dirt, debris, mold, and bacteria from the system. Throughout the paper, the critical parameters and control points of the air handling units for hospitals are analyzed from a hygienic viewpoint, and the existing hygienic design standards are explained through an implemented case study.