An antimicrobial is an agent that kills microorganisms (microbicide) or stops their growth (bacteriostatic agent). Antimicrobial medicines can be grouped according to the microorganisms they are used to treat. For example, antibiotics are used against bacteria, and antifungals are used against fungi. They can also be classified according to their function. Antimicrobial medicines to treat infection are known as antimicrobial chemotherapy, while antimicrobial drugs are used to prevent infection, which known as antimicrobial prophylaxis.

The main classes of antimicrobial agents are disinfectants (non-selective agents, such as bleach), which kill a wide range of microbes on surfaces to prevent the spread of illness, antiseptics which are applied to living tissue and help reduce infection during surgery, and antibiotics which destroy microorganisms within the body. The term antibiotic originally described only those formulations derived from living microorganisms but is now also applied to synthetic agents, such as sulfonamides or fluoroquinolones. Though the term used to be restricted to antibacterials, its context has broadened to include all antimicrobials. In response, further advancements in antimicrobial technologies have resulted in solutions that can go beyond simply inhibiting microbial growth. Instead, certain types of porous media have been developed to kill microbes on contact. The misuse and overuse of antimicrobials in humans, animals and plants are the main drivers in the development of drug-resistant pathogens. It is estimated that bacterial antimicrobial resistance (AMR) was directly responsible for 1.27 million global deaths in 2019 and contributed to 4.95 million deaths.

Antimicrobial use has been common practice for at least 2000 years. Ancient Egyptians and ancient Greeks used specific molds and plant extracts to treat infection.

In the 19th century, microbiologists such as Louis Pasteur and Jules Francois Joubert observed antagonism between some bacteria and discussed the merits of controlling these interactions in medicine. Louis Pasteur's work in fermentation and spontaneous generation led to the distinction between anaerobic and aerobic bacteria. The information garnered by Pasteur led Joseph Lister to incorporate antiseptic methods, such as sterilizing surgical tools and debriding wounds into surgical procedures. The implementation of these antiseptic techniques drastically reduced the number of infections and subsequent deaths associated with surgical procedures. Louis Pasteur's work in microbiology also led to the development of many vaccines for life-threatening diseases such as anthrax and rabies. On September 3, 1928, Alexander Fleming returned from a vacation and discovered that a Petri dish filled with Staphylococcus was separated into colonies due to the antimicrobial fungus Penicillium rubens. Fleming and his associates struggled to isolate the antimicrobial but referenced its therapeutic potential in 1929 in the British Journal of Experimental Pathology. In 1942, Howard Florey, Ernst Chain, and Edward Abraham used Fleming's work to purify and extract penicillin for medicinal uses earning them the 1945 Nobel Prize in Medicine.

Antibacterials are used to treat bacterial infections. Antibiotics are classified generally as beta-lactams, macrolides, quinolones, tetracyclines or aminoglycosides. Their classification within these categories depends on their antimicrobial spectra, pharmacodynamics and chemical composition. Prolonged use of certain antibacterials can decrease the number of enteric bacteria, which may have a negative impact on health. Consumption of probiotics and healthy eating may help to replace destroyed gut flora. Stool transplants may be considered however for patients who are having difficulty recovering from prolonged antibiotic treatment, such as recurrent Clostridioides difficile infections.

The discovery, development and use of antibacterials during the 20th century have reduced mortality from bacterial infections. The antibiotic era began with the therapeutic application of sulfonamide drugs in 1936, followed by a "golden" period of discovery from about 1945 to 1970, when a number of structurally diverse and highly effective agents were discovered and developed. Since 1980, the introduction of new antimicrobial agents for clinical use has declined, in part because of the enormous expense of developing and testing new drugs. In parallel, there has been an alarming increase in antimicrobial resistance of bacteria, fungi, parasites and some viruses to multiple existing agents.

Antibacterials are among the most commonly used and misused drugs by physicians, for example, in viral respiratory tract infections. As a consequence of widespread and injudicious use of antibacterials, there has been an accelerated emergence of antibiotic-resistant pathogens, resulting in a serious threat to global public health. The resistance problem demands that a renewed effort be made to seek antibacterial agents effective against pathogenic bacteria resistant to current antibacterials. Possible strategies towards this objective include increased sampling from diverse environments and application of metagenomics to identify bioactive compounds produced by currently unknown and uncultured microorganisms as well as the development of small-molecule libraries customized for bacterial targets.

Antifungals are used to kill or prevent further growth of fungi. In medicine, they are used as a treatment for infections such as athlete's foot, ringworm and thrush and work by exploiting differences between mammalian and fungal cells. Unlike bacteria, both fungi and humans are eukaryotes. Thus, fungal and human cells are similar at the molecular level, making it more difficult to find a target for an antifungal drug to attack that does not also exist in the host organism. Consequently, there are often side effects to some of these drugs. Some of these side effects can be life-threatening if the drug is not used properly.