As in pharmaceutical applications, concern in the health care field is focused on control of viable microorganisms. The original goal of contamination control measures was to protect patients from exposure to harmful microorganisms having the potential to complicate their recovery from their presenting illnesses. More recently, this concern has expanded to include protection of health care workers from exposure to life-threatening diseases resulting from patient contact. Strains of the tuberculosis bacterium that are resistant to the standard anti-tuberculosis drugs have caused deadly outbreaks in five states and at least one case in eight other states. The Centers for Disease Control has described the spread of the disease as "out of control," and has summoned TB experts and health officials from 46 states to begin devising a national strategy against the disease. The disease, which is spread in aerosol droplets dispersed through the air by coughing, is expected to present a particular hazard to health care workers who must deal with infected patients.

The microbes of concern are primarily bacteria such as the TB bacillus and viruses. Bacteria are usually present in Colony Forming Units (CFUs) greater than one micron in diameter, so standard HEPA filters offer close to 100 percent effective control. Viruses are much smaller, usually in the 0.003 to 0.05 µm range. Availability of a filter technique effective in this size range is regarded as a development that would greatly expand the applicability of cleanrooms in health care environments.

The first use of cleanrooms in the health care field was in operating rooms. Initially, their use was widely adopted only in orthopedic surgeries. The long duration of orthopedic operations increased the likelihood that the wound site would become colonized by pathogenic organisms during the course of surgery. Because orthopedic prostheses and implants are frequently cemented onto adjacent bone, redoing the surgery to treat a serious infection is often not feasible.

Other areas where cleanrooms are being put into use include delivery rooms, nurseries, burn units, intensive and cardiac care units, and facilities in which immunosuppressed patients are cared for. One of the latest advances is the use of cleanrooms in dental surgery facilities to decrease the risk of infection to the staff during long surgeries.

The aging of the population is expected to continue to drive a general expansion of the health care sector, and health care cleanroom applications are expected to participate in the general expansion.

According to the "Draft Guideline for the Prevention of Surgical Site Infection" (SSI), operating rooms should be maintained at positive pressure with respect to corridors and adjacent areas. Positive pressure prevents air flow from less clean areas into clean areas. All ventilation or air conditioning systems in hospitals, including those in operating rooms, should have two filter beds in series with the efficiency of filter bed one 30 percent and filter bed two 90 percent. Conventional operating room ventilation systems produce a minimum of about 15 air changes of filtered air per hour. Three (20 percent) of these air changes/hour must be fresh air. Air should be introduced at the ceiling and exhausted near the floor. Recommended ventilation parameters for operating rooms have been published by the American Institute of Architects, and the U.S. Department of Health and Human Service.

Laminar air flow is designed to move particle-free air (called "ultraclean air") over the aseptic operating field at a uniform velocity (0.3 to 0.5 µm/sec), sweeping away particles in its path. This air flow can be directed vertically or horizontally, and recirculated air is usually passed through a high efficiency particulate air (HEPA) filter. HEPA filters, commonly used in hospitals, remove particles 0.3 µm in diameter with an efficiency of 99.97 percent. Ultraviolet (UV) light has been used as an infection control measure to reduce SSI risk. However, neither laminar flow nor UV light has been conclusively shown to decrease overall SSI risk.