Aim: Establish the influence of the terminal or nonterminal position of High Efficiency Particulate Air (HEPA) filters in the Heating, Ventilation, and Air Conditioning (HVAC) system on the presence of airborne fungi in controlled environment rooms. Background: Fungal infections are an important cause of morbidity and mortality in hospitalized patients. Methods: This study was realized from 2010 to 2017, in rooms with terminal and nonterminal HEPA filters, in eight Spanish hospitals. In rooms with terminal HEPA filters, 2,053 and 2,049 samples were recollected, and in rooms with nonterminal HEPA filters, 430 and 428 samples were recollected in the air discharge outlet (Point 1) and in the center of the room (Point 2), respectively. Temperature, relative humidity, air changes per hour, and differential pressure were recollected. Results: Multivariable analysis showed higher odds ratio ( OR) of airborne fungi presence when HEPA filters were in nonterminal position ( OR: 6.78; 95% CI [3.77, 12.20]) in Point 1 and ( OR: 4.43; 95% CI [2.65, 7.40]) in Point 2. Other parameters influenced airborne fungi presence, such as temperature ( OR: 1.23; 95% CI [1.06, 1.41]) in Point 2 differential pressure ( OR: 0.86; 95% CI [0.84, 0.90]) and ( OR: 0.88; 95% CI [0.86, 0.91]) in Points 1 and 2, respectively. Conclusions: HEPA filter in terminal position of the HVAC system reduces the presence of airborne fungi. To decrease the presence of airborne fungi, adequate maintenance of the environmental and design parameters is necessary in addition to the terminal position of the HEPA filter.