During the decades before the Civil War, larger cities in the United States and elsewhere had faced rapidly growing populations and population densities, with an associated increase in disease epidemics. Although it would be several more decades before microbes were proven to be the causes of many diseases, some physicians, sanitarians, and other reformers had begun to collect and analyze data that correlated poverty, poor housing, lack of clean water, and filthy environments with increased rates of disease and death.

During the Crimean War and U.S. Civil War, the success of sanitary practices--cleanliness, good drainage, use of disinfectants--in reducing illness and wound infections slowly convinced military and civilian leaders to incorporate them into standard disease-fighting strategies--or at least, not to dismiss them as irrelevant. Many physicians who served in Hammond’s reformed army medical department got hands-on training not just in diagnosis and surgery but in the best current sanitation practices. They returned to civilian practice with better skills and an appreciation of public health measures, and often became involved in sanitary reform.

New York City, hoping to limit the risks of infectious disease, was the first city to develop a permanent municipal public health infrastructure. It was the largest U.S. city, and had been growing rapidly since the 1840s. Increased immigration from Ireland and other countries strained existing city services; during and after the Civil War, migrating freedmen added to these numbers. New York was also home to many of America’s foremost physicians as well as leading social and sanitary reformers. The New York Sanitary Association was established in 1859, by some of the same people who helped set up the USSC several years later. In 1863, a group of reformers founded the New York Citizens Association to address a number of issues, and it absorbed the Sanitary Association. These reformers introduced public health bills to the state legislature in 1857, 1860, and 1861, but these did not pass, and the start of the Civil War delayed work on further bills for several years.

In 1864, the Citizens Association introduced another public health bill to the New York state legislature, and asked local physicians for their support. The physicians, in turn, organized a Special Council of Hygiene and Public Health, which appointed a committee to do a sanitary survey of New York City. Thirty-one medical inspectors, one to each “sanitary district,” spent several months gathering data not only about death rates and cases of various illnesses, but about the physical environments of the districts: the condition and density of the housing, the quality of water supply, sewage and trash disposal, ventilation, and the presence of businesses such as slaughterhouses, stables, etc. Where they found cases of disease, inspectors collected data about the patients, including ethnicity, occupation, habits, income level, and apparent intelligence. With this information, (which filled seventeen volumes of reports the committee was able to demonstrate in detail many of the preventable causes of disease and excess mortality in the city. When epidemic cholera again threatened the city in late 1865, a condensed version of the reports helped convince skeptical politicians to pass the Metropolitan Health Act, which established the Metropolitan Board of Health of New York City in February of 1866. The Board’s successful handling of the 1866-67 cholera epidemic helped the cause of sanitary reform enormously. Other large cities, including Chicago, Cincinnati, and St. Louis, followed the New York example, conducting sanitary surveys and establishing permanent public health boards during the 1870s and beyond. It was a slow process; sanitary reform still took a long time to sell to politicians and taxpayers, because it meant paying for the initial cleanups and infrastructure, and then for maintenance.

New York’s Metropolitan Board of Health activities attracted inquiries from physicians and sanitarians in many other American cities, signaling a need for a national organization. In 1872, public health leaders founded the American Public Health Association. The new organization’s goal was to advance sanitary science and promote organizations and measures for the practical application of public hygiene. One of its first endeavors was to send questionnaires to every town with over 5,000 residents. These covered virtually every subject of concern to community health--including the town’s altitude, the number of paved streets, and the ventilation of public buildings. The survey requested detailed information about water supplies, sewer systems, vital statistics, and the community’s health agency, if it had one. The response rate to this survey wasn’t as good as the APHA hoped (for a number of reasons) and reports on its progress (in the annual volume Public Health: Papers and Reports of the American Public Health Association) indicated that the organization lacked the funds to fully pursue and analyze the data. Nonetheless, it was an important step in assessing the state of public health agencies across the country, and also in learning more about the common obstacles to improvements.

By the last decades of the 1800s, there was increasing support for sanitary reform at local and state levels. As towns and cities grew and experienced the tragic and disruptive effects of epidemic diseases, the value of sanitary improvements became clearer, especially as germ theory of disease gained acceptance. Business and civic organizations became supporters of public health measures as they gradually recognized that a reputation for unhealthy environments would be bad for a city’s commerce and community growth. Gradually, cities and states established permanent boards of health, which collected all sorts of data--vital statistics, building and sewer inspections, etc. as well as tracking the health of students in the public school systems.

In contrast to England and many European countries, the United States did not centralize its public health administration in the nineteenth century. Most of the public health authority was held by state and local governments. However, in the wake of yellow fever epidemics throughout the Mississippi Valley in 1878, many members of the APHA and the American Medical Association supported the idea of a federal-level agency that could coordinate quarantine efforts and advise states and municipalities. The National Board of Health was established by Congress in 1879, for a four-year term. Among its activities were grants to public health departments in cities such as New Orleans and a sanitary survey of Memphis, Tennessee, which was decimated by yellow fever in 1978-79.

The National Board of Health had a short life; it failed to gain permanent status and funding, and its leaders could not develop acceptable rationales for national authority. By the end of the 1800s, however, a de facto national health agency had evolved with the expansion of the Marine Hospital Service. It had been established in 1798 to provide shore care for sailors serving on merchant and U.S. Navy ships, but after the Civil War, the responsibilities of the MHS expanded. Commerce and shipping increased as America’s population and economy grew, with a corresponding need for marine hospitals. With more immigration and more densely populated cities, the risk of epidemic diseases such as cholera, smallpox, and yellow fever also grew. Medical practitioners were only starting to accept the “germ theory” of disease, i.e., that microbes (bacteria, viruses, etc.) caused many illnesses; medical researchers were just beginning to identify the microbes that caused specific diseases. By the early twentieth century the causative organisms of many diseases (including cholera, tuberculosis, typhoid, diphtheria, plague, and pneumonia) would be identified, and advances in microbiology would yield vaccines or anti-toxin treatments for some of them. But this took several decades to achieve. Meanwhile, the experiences of early public health workers, military doctors and nurses, and others had demonstrated that cleanliness and proper handling of waste could reduce the transmission of many diseases, even if it wasn’t clear what caused them. Quarantine of ships, cargo, and passengers--one of the oldest ways to limit infectious disease spread--became more effective as local, state, and federal officials applied the new public health knowledge. In 1878, the National Quarantine Act made the MHS responsible for all maritime quarantine, and for general disease surveillance. In 1887, a Hygienic Laboratory was established at the MHS hospital on Staten Island to conduct bacteriological testing for diseases such as cholera and do research. It was moved to Washington, DC in 1891 and soon expanded its activities to include bacteriological training for federal and state public health officers, production of antitoxins, regulation of vaccine production, and field investigations of diseases ranging from plague to Rocky Mountain spotted fever. (The MHS was renamed the Public Health and Marine Hospital Service in 1902, and became the U.S. Public Health Service in 1912.)

In the 1880s, the MHS began assigning officers to strategic observation posts in Asia and South America as well as Europe, to keep up on information about epidemics in those regions. Their observations were recorded in the Weekly Abstracts of Sanitary Reports tracking epidemic diseases, which the MHS started publishing in 1887. At first, these were short tables showing incidence of diseases in many major world ports, with occasional special reports on individual disease outbreaks. Later, the public health reports would also include statistics from many American cities, and the results of field investigations by PHS staff.

Immigration inspections--another type of risk assessment--also became part of the MHS responsibility after 1890. Between 1870 and 1900, over 11 million people immigrated to the United States, many drawn by opportunities for industrial or farming work and some fleeing persecution in their native countries. While employers were glad for their labor, the vast number of immigrants provoked several concerns. Many, especially public health officials, worried that they might be carrying diseases when they arrived, and provide breeding grounds for disease in the overcrowded and dilapidated urban neighborhoods where they often settled. Likewise, proponents of recent evolutionary and hereditary theories worried that immigrants might bring undesirable genetic legacies, heritable mental or physical disabilities that they might pass on to the next generation, thereby degrading America's "racial stock." Government officials feared that any of these problems might render immigrants unable to support themselves in their new home, placing economic burdens on the community. A new immigration law passed in 1891 mandated the health inspection of all immigrants and stipulated that Marine Hospital Service officers should do the inspections. The law specified that “all idiots, insane persons, paupers or persons likely to become public charges, persons suffering from a loathsome or dangerous contagious disease,” as well as criminals, were to be excluded. The immigration inspectors later helped develop and test a number of intelligence evaluation methods and tools, to help screen out “feebleminded” would-be immigrants.