Why Militaries Vaccinate
History has already answered the question of what happens when they stop.
On April 21, 2026, the U.S. Secretary of Defense signed a memorandum making the annual influenza vaccine voluntary for all active-duty service members, reservists, and Department of Defense civilians. The justification was “medical autonomy” and religious freedom. From the announcement itself: “The notion that a flu vaccine must be mandatory for every service member, everywhere, in every circumstance at all times is just overly broad and not rational.”
For context, influenza vaccination has been mandatory for U.S. military personnel since the 1950s, with the Department of Defense historically targeting over 90% annual coverage.
As an infectious diseases physician, I find this decision baffling, not because I am reflexively pro-vaccine, but because history has already answered the question of what happens when militaries lose control of infectious disease.
Before bullets, there was disease
For the first 145 years of U.S. military history, far more personnel died from infection than from combat. Historians have formalized this into two periods: the Disease Era (1775–1918) and the Trauma Era (1941–present). During the Civil War, roughly two-thirds of the 660,000 military deaths were caused by pneumonia, typhoid, dysentery, and malaria. In the Mexican-American War, disease accounted for an estimated 88% of U.S. deaths. During the Napoleonic Wars, British soldiers were eight times more likely to die of disease than of a battle wound.
The turning point came with World War II, which coincided with two of the most transformative advances in medical history: antibiotics and mass vaccination. By the 1940s, militaries were systematically deploying vaccines against yellow fever, tetanus, typhoid, and influenza. Penicillin was available to treat wounded soldiers. Sanitation and vector control were no longer afterthoughts. World War II was the first major American war in which combat killed more soldiers than disease and military vaccination policy is a large part of why that was true.
The first mandate: Washington and smallpox
In February 1777, George Washington ordered the mandatory variolation of the Continental Army against smallpox. It was the first mass immunization policy in U.S. history, and it came after a devastating outbreak had already crippled American forces during the Quebec campaign. British troops, largely immune from childhood exposure, held a decisive biological advantage. Washington described smallpox as “more destructive than the sword.” Many historians credit his decision with preserving the Continental Army long enough to win the war. It is worth pausing on that. The founding act of American military medicine was a vaccine mandate.
Barracks epidemiology hasn’t changed
The Civil War offers the second lesson. Measles killed at least 4,246 Union soldiers, with case fatality rates of 6% in white soldiers and 11% in Black soldiers. Immunologically naïve recruits from rural communities were packed into crowded camps, placed under intense physical stress, and shipped around the country. Outbreaks were so predictable that they were treated as a phase of training , a rite of passage called “seasoning.” Modern recruits face the same conditions. Young adults, from different regions, in close quarters, under physiologic stress, are the ideal marinade for an outbreak. What has changed is not the epidemiology of infectious diseases but the availability of vaccines to blunt their effects and offer reliable protection.
1918: the military as a global amplifier
The 1918 influenza pandemic remains the clearest example of what happens when infectious disease intersects with military logistics. The outbreak is conventionally traced to Camp Funston, Kansas in March 1918. Within weeks, ~1,100 of 56,000 troops there were sick, and outbreaks had reached 24 of 36 major U.S. training camps. At Camp Devens in Massachusetts, 14,000 soldiers a quarter of the camp were infected by September. From there, troop movements seeded outbreaks across the United States and the world. Rail networks, ports, and troopships turned military logistics into a transmission network. In India, the virus traveled inland on trains carrying returning soldiers. African ports receiving demobilizing troops saw case numbers explode within weeks South Africa and Kenya each lost an estimated 4–6% of their populations. The U.S. numbers alone estimate approximately 26% of the U.S. Army infected, more than a million soldiers, roughly 45,000 military deaths, and 675,000 civilian deaths more than the United States lost in WWI, WWII, Korea, and Vietnam combined. The military was not just affected by the 1918 pandemic it amplified it well beyond the borders of the U.S.
Adenovirus: the modern warning
If WWII shows us what happens when you control infectious disease in a military population, adenovirus shows what happens when you stop. For decades, U.S. recruits received an oral vaccine against adenovirus types 4 and 7. In 1996, the sole manufacturer stopped production. By 1999, the stockpile was depleted and vaccination ceased. Between 1999 and 2010, the military recorded roughly 110,000 febrile respiratory illnesses among recruits, 73,000 confirmed adenovirus cases, and 8 deaths. Each year without the vaccine produced resulted in on average, one death, 1,100 to 2,700 hospitalizations, and about 13,000 infections. When a replacement vaccine was licensed in 2011, case rates dropped dramatically and have stayed low since. This is as close to a controlled experiment as public health ever gets. Same population, same bases, same pathogen. Vaccine off, cases up. Vaccine back on, cases down. It is also the closest historical analog we have to the decision made this week.
Why this never stays “in the military”
Militaries are not closed systems. The health of a military population directly shapes the health of the communities around it. Service members live with families. They share base schools, base clinics, and base commissaries. They travel home on leave, eat in local restaurants, use local hospitals, and work alongside civilian contractors. In the coastal towns around Norfolk, outside Fort Liberty, around Camp Pendleton, in the communities encircling U.S. bases in Germany, Japan, and Korea, the epidemiology of the base is the epidemiology of the surrounding county. When you drop a base’s vaccination coverage below the threshold required for herd immunity, the county becomes more vulnerable to whatever that base is currently incubating.
The amplification problem also runs in the other direction. U.S. service members deploy to regions with pathogens their home populations have not encountered in generations. For example yellow fever in West Africa and South America, Japanese encephalitis in parts of Asia, typhoid and cholera in low-sanitation environments. When they come home, they come with their microbiome and their exposures. The 1918 pattern clearly demonstrated the ability of troops to carry a virus from port to port, from camp to home, from military depot to civilian rail line. It is not a historical artifact but rather a template that modern logistics would make more efficient.
A personal aside
A few weeks ago, while on clinical service, I got a call from one of the teams with a new consult: “Young active duty military service member, presenting with unexplained seizures — we are concerned for rabies.”
After a good chuckle at an overly enthusiastic intern (rabies is exceedingly rare in the U.S. and the exposure history did not fit), I told the team, very confidently: If this individual is an active duty service member in the U.S. Army, they are vaccinated against rabies. You can be sure of that.
That certainty came from the U.S. military’s long, disciplined, boring, expensive history of protecting its own people from preventable infection , the same history that made rabies a footnote to an intern’s case presentation rather than a real possibility in a young American soldier with seizures.
The flu vaccine reversal is, on its face, limited. One vaccine. One population. Exemption windows for branches that choose to keep it. But vaccine policy rarely retreats in a single step, and rarely retreats in isolation.
The open question is not only what this means for the U.S. military. It is what it means for the populations that military is stationed within, deploys to, and ultimately comes home to. What we can say with certainty is this: lower influenza vaccination coverage in the military will mean more sick soldiers next season, and more preventable complications in otherwise young, healthy individuals. History has already shown us how this story ends when vaccines are withdrawn. Ignoring it does not change the outcome. It only ensures that when it happens again, it will not be a surprise it will be a choice.
I am an infectious disease physician and global health researcher who writes at the intersection of medicine, science, and justice. Please subscribe and share this post if you found it informative.