[8] In healthcare settings, these sanitizers are often preferred over hand washing with soap and water because they are more effective at reducing bacteria and are better tolerated by the skin.

[11] Non-alcohol-based hand sanitizers, which may contain benzalkonium chloride or triclosan, are less effective and generally not recommended,[9] though they are not flammable.

[4] To prevent skin dryness, compounds such as glycerol may be added, and some formulations include fragrances, though these are discouraged due to the risk of allergic reactions.

[16] Alcohol-based hand sanitizers became commonly used in Europe by the 1980s[17] and have since been included on the World Health Organization's List of Essential Medicines.

[23] In a 2020 Cochrane review comparing rinse-free hand washing to conventional soap and water techniques and the subsequent impact on school absenteeism found a small but beneficial effect on rinse-free hand washing on illness related absenteeism.

[26][31] In too low quantities (0.3 ml) or concentrations (below 60%), the alcohol in hand sanitizers may not have the 10–15 seconds exposure time required to denature proteins and lyse cells.

[32][33] Products with alcohol concentrations as low as 40% are available in American stores, according to researchers at East Tennessee State University.

[30] For health care, optimal disinfection requires attention to all exposed surfaces such as around the fingernails, between the fingers, on the back of the thumb, and around the wrist.

[30] There are certain situations during which hand washing with soap and water are preferred over hand sanitizer, these include: eliminating bacterial spores of Clostridioides difficile, parasites such as Cryptosporidium, and certain viruses like norovirus depending on the concentration of alcohol in the sanitizer (95% alcohol was seen to be most effective in eliminating most viruses).

Some hand sanitizer gels may not produce this effect due to a high concentration of water or moisturizing agents.

[4]: 13  Hand sanitizer should be stored in temperatures below 105 °F and should not be left in a car during hot weather due to risk of flammability.

[45] Fire departments suggest refills for the alcohol-based hand sanitizers can be stored with cleaning supplies away from heat sources or open flames.

[52] In clinical trials, alcohol-based hand sanitizers containing emollients caused substantially less skin irritation and dryness than soaps or antimicrobial detergents.

[31] The lower tendency to induce irritant contact dermatitis became an attraction as compared to soap and water hand washing.

[63][64] In 2021, a dozen children were hospitalized in the state of Maharashtra, India, after they were mistakenly orally administered hand sanitizer instead of a polio vaccine.

[67] Some hand sanitizer products use agents other than alcohol to kill microorganisms, such as povidone-iodine, benzalkonium chloride or triclosan.

Both substantive and nonsubstantive active ingredients can show a persistent effect if they substantially lower the number of bacteria during the wash period.

[77] For DCDD, one of the non-toxic compounds of the dioxin family,[78] a conversion rate of 1% has been reported and estimated half-lives suggest that it is photolabile as well.

[79] The formation-decay kinetics of DCDD are also reported by Sanchez-Prado et al. (2006) who claim "transformation of triclosan to toxic dioxins has never been shown and is highly unlikely.

In June 2009, alcohol-free Clarcon Antimicrobial Hand Sanitizer was pulled from the US market by the FDA, which found the product contained gross contamination of extremely high levels of various bacteria, including those which can "cause opportunistic infections of the skin and underlying tissues and could result in medical or surgical attention as well as permanent damage".

[30] The hand sanitizer dosing systems for hospitals are designed to deliver a measured amount of the product for staff.

Dispensers for surgical hand disinfection are usually equipped with elbow controlled mechanism or infrared sensors to avoid any contact with the pump.

[86][87] In the beginnings of the pandemic, because of hand sanitizer shortages due to panic buying, people resorted to using 60% to 99% concentrations of isopropyl or ethyl alcohol for hand sanitization, typically mixing them with glycerol or soothing moisturizers or liquid contain aloe vera to counteract irritations with options of adding drops of lemon or lime juice or essential oils for scents, and thus making DIY hand sanitizers.

[88] However, there are cautions against making them, such as a wrong measurement or ingredient may resulting in an insufficient amount of alcohol to kill the coronavirus, thus rendering the mixture ineffective or even poisonous.

[89] Additionally, some commercial products are dangerous, either due to poor oversight and process control, or fraudulent motive.

[90] Products suspected of manufacture by Eskbiochem SA with excessive methanol have been reported as far away as British Columbia, Canada.