Numerous non-incineration methods are available to treat infectious waste. The most common is autoclaving, which uses high-pressure steam, usually at 121-134 °C, to disinfect waste so that it can be recycled or disposed of safely. Microwaves are also increasingly common; they deactivate pathogens with steam, although at atmospheric temperature.

Autoclaving is a highly flexible technology that many hospitals are familiar with. It is used for sterilizing surgical instruments and many other products. Autoclaves are easy to operate, maintain, and monitor. The majority of autoclaves operate on electrical power, but steam can also be generated with other fuels, predominantly gas.

• Other treatment technologies use steam or dry heat as a disinfection agent. All of these operate below 180°C and do not change the physical or chemical form of the waste. As a result, they produce little or no pollution, though care must be taken to ensure that wastes containing volatile chemicals, such as solvents and mercury, are not treated this way as they will be emitted into the atmosphere.
• Chemical disinfectants are used by several technology providers. However, the majority of these involve persistent pollutants that will be emitted with the treated waste. An exception is ozone treatment, as this rapidly breaks down to oxygen. 
• Biological methods include natural breakdown in placenta pits. Biodigesters, using anaerobic bacteria, can be used for larger quantities of placentas, often combined with kitchen wastes. Vermiculture (worm composting) has been tested for soft waste such as used bandages, again in combination with food waste.

Sharps waste is a subset of infectious waste and comprises syringes, needles, lancets, broken glass, and any other materials that can pierce the skin. The combination of contamination with pathogens and the ability to break through the skin’s protection makes them one of the most dangerous wastes produced in health care settings:

• The vast majority of sharps waste is syringes from the approximately 16 billion injections given each year. Between December 2020 and December 2022, another 13 billion COVID-19 vaccinations were delivered. 
• Vaccinations are essential to prevent disease, but over 50% of the curative injections given each year are not necessary as they could be replaced by oral medications.
• Reuse of syringes causes millions of infections each year, with HIV, hepatitis, and bacterial infections. To try to reduce this, WHO recommends using auto-disable syringes during vaccination programs. However, these can still cause injury, and 10-20% of needle stick injuries happen during disposal, making proper management essential. 

Needle cutters - also called hub cutters - which cut off the needle and the end of the syringe so that it cannot be used again, can prevent reuse and make treatment and disposal safer and easier. “Defanged” syringes can then easily be autoclaved or disinfected with any of the technologies used for infectious waste. 

In addition, some waste treatment companies provide reusable sharps containers that can be disinfected with their contents and returned to use.

Disposing of pharmaceutical and other chemical waste, such as laboratory waste, can be highly problematic if there are no established treatment facilities.

One of the simplest steps is to minimize waste by careful stock-keeping. Keep a record of the amount of each medicine that is needed and avoid ordering too much to prevent it from going out of date. Purchasers or prescribers can choose pharmaceuticals that have been shown to have lower environmental persistence, in a database created and maintained by the Stockholm County Council, which is available in Swedish and English. Health care facilities or large-scale organizations, such as the United Nations or government agencies can also negotiate take-back agreements with suppliers, where suppliers accept and dispose of pharmaceuticals that their customers cannot use.

Various treatment and disposal options are available for different situations. Cheap and easily obtained chemicals can neutralize specific drugs, particularly chemotherapeutic agents. Many are listed in the Annexes of the WHO Guidelines on the Safe Management of Wastes from Healthcare Facilities:

• The WHO has long recommended inertization and encapsulation procedures in emergency situations, which are applicable to low-resource environments. Inertization involves taking the pills out of the packaging, mixing them with liquid concrete, and depositing the concrete in a landfill.
• Encapsulation involves putting the pharmaceuticals into barrels, which are then filled with concrete and landfilled. This can be done more cheaply and quickly since the pills will not have to be taken out of the PVC blister packs they are usually supplied in. These packs are not recyclable, so no useful resources are wasted.
• Alkaline hydrolysis allows breaking down animal tissues, killing pathogens including prions, and destroying hazardous chemicals such as formaldehyde and chemotherapy drugs. More research is needed to validate its use for specific pharmaceuticals. It is cost-competitive with incineration using air pollution control.

Not all facilities produce radioactive waste, but it can result from treatment (for example, radioactive tracers) or be present in diagnostic and analytical equipment. Many radionuclides used in medicine degrade rapidly. Suppliers of medical or laboratory equipment containing radioactive sources should collect and manage these when they are no longer needed.

Pathological and anatomical wastes include everything from lab cultures and stocks to donated blood and tissue collected for testing or removed during surgery. Anatomical waste is a subtype of pathological waste, being recognizably human materials, such as an amputated limb. Some of this waste, such as placentas from healthy mothers or expired blood, may not be infectious, but unless its status is known, it is treated as though it were.

The most appropriate treatment can depend on cultural factors as well as practical ones. For example, in some places, it is traditional to bury the placenta in the grounds of the home. Similarly, in some cases, an amputated limb may be buried or cremated in the same way as a dead person, and in others, it is regarded as waste to be disposed of. These considerations should come first unless there is a risk of disease transmission.

• Lab cultures and stocks are the most dangerous of these wastes and should be autoclaved as close to their source as possible, ideally in the microbiology department itself. Tissue digesters can also be used for this and indeed, any type of pathological waste, but these are far more expensive and less widely available than autoclaves. Note that autoclaving is only suitable for small volumes, such as culture tubes. The steam cannot easily heat larger items, so it will not be effective.
• Placenta pits allow disposing of pathological waste, using a combination of natural chemical and biological decomposition processes. They can be perfectly effective if they are well designed and constructed but may not be suitable for urban areas, close to water sources, or where the groundwater is near the surface.
• Where there is an adequate sewage treatment system—even a well-functioning septic system—it is possible to dispose of some types of pathological waste in the sewer. Blood and placentas are the most likely candidates for this route.
• Biodigestion is a possibility for pathological wastes such as placentas. This technology is widely used for agricultural waste and can be adapted for health care settings. As a bonus, this disposal method also generates biogas which can be used as a fuel.

As much as 25 percent of the waste from a health care facility can be kitchen and food scraps. These can be composted or biodigested to produce compost and biogas, a renewable fuel. 

Paper, plastic, metal, and glass are the most widely recycled materials. Segregating, repurposing, and recycling these materials can significantly improve the economics of a facility's waste disposal operation. Any potentially hazardous medical waste, such as used syringes or gloves, must be very carefully treated before recycling to ensure that it is no longer harmful and can never be reused.