The health care sector is far from the greatest source of organic mercury compounds in the environment. Rather, coal-fired power plant emissions and mercury cell chlor-alkali plants, along with artisanal gold mining and battery disposal are all far more significant polluters. However, the health care sector does play an important role as a source of global emissions, as well as a source of low-level, chronic and acute elemental mercury poisoning.

Mercury can be found in many health care devices and present in fluorescent lamps as well as dental amalgams. Mercury is also found in many chemicals and measurement devices used in health care laboratories. Medical waste incinerators, as well as municipal waste incinerators, emit mercury into the atmosphere when they burn wastes that contain mercury. According to the U.S. Environmental Protection Agency (EPA), in 1996, prior to the mercury phase-out in U.S. health care, medical waste incinerators were the fourth largest source of mercury emissions to the environment. Hospitals were also known to contribute 4-5% of the total wastewater mercury load. And mercury fever thermometers alone contributed about 15 metric tons of mercury to solid waste landfills annually.

In 2005, Transande et. Al. using national blood mercury prevalence data from the US Centers for Disease Control estimated that between in this century 316,588 and 637,233 US children each year have cord blood mercury levels > 5.8 µg/L, a level associated with loss of IQ. They estimated that lost productivity due to this amounts to $8.7 billion annually (range, $2.2–43.8 billion).

While no comprehensive figures are available, anecdotal evidence suggests that in most of Asia, Africa and Latin America, mercury spills are not properly cleaned, nor is the waste segregated and managed properly. Rather, it is either incinerated, flushed down the drain, or sent, via solid waste, to a landfill.

Thermometer breakages on a case-by-case basis pose some harm to patients, nurses and other health care providers when mercury is absorbed through the skin or mercury vapour is inhaled. Only a relatively small amount of mercury roughly one gram is released when each thermometer breaks. However, when taken cumulatively on a hospital ward, in an entire hospital, nationally and globally, the situation takes on more serious dimensions.

In Buenos Aires, for instance, the city government, which runs 33 hospitals and more than 38 clinics, was purchasing nearly 40,000 new thermometers a year, until it began to switch over to alternatives in 2006. Given that nurses and other health care professionals often buy their own thermometers to supplement the city's procurement, the city's health system was using well over 40,000 thermometers a year, most of which would break, and some of which would be taken home (where most would ultimately break as well). The system was ultimately emitting in excess of 40 kilograms of mercury into the local hospital environment and into the global ecosystem every year.

If one were to use this figure and extrapolate for the entire country, one can estimate that until recently thermometers broken in Argentina's health care system were spilling 826 kilos, or nearly 1 metric ton of mercury, into the global environment every year.

In Mexico City, the 250-bed Federico Gomez Children's Hospital is a medical service, teaching, and research hospital affiliated with the National Autonomous University of Mexico. This prestigious children’s hospital documented a thermometer breakage rate of 385 per month, or well over 4,000 per year. The total number of estimated broken thermometers in this one hospital between 2002 and early 2007 is nearly 22,000—the equivalent of 22 kilograms of mercury.

While the Federico Gomez hospital has now substituted its mercury devices with alternatives, when it undertook its initial assessment there was no clean-up protocol for mercury spills. Rather, mercury waste was deposited with both infectious and biological hazardous wastes, or with municipal wastes. Broken fluorescent lamps were also treated as municipal waste. Mercury containing equipment was not repaired if broken, and the procedure followed was to merely register the loss and replace it with new equipment.

The regular and ongoing breakage of thermometers and the lack of mercury waste management protocols and practices found at the Federico Gomez hospital is not an exception, but more generally the rule in hospitals throughout much of the Global South, where patients and health care workers are regularly and unknowingly exposed to this toxin.