The Jacobson decision did not resolve the controversy over vaccination. Lurking in its background is the fact that vaccination had been practiced for over a century, yet smallpox continued to plague American communities because people did not routinely get it done. Although medical societies and health authorities enthusiastically endorsed vaccination, the general population did not seem to regard it with much favor, and information available for Boston and other Massachusetts communities indicates that people seemed to avoid it until compelled or coerced into it by the law or their employers. Parents waited until their children reached school age, and they did not apparently revaccinate at adolescence. The Jacobson decision alone did little to change that pattern. In 1909 the Boston Medical and Surgical Journal still had to urge people and medical practitioners to vaccinate and revaccinate when the tetanus death of a local child after vaccination reinvigorated public anxiety about school vaccinations.

From its inception, vaccination was never as simple, foolproof, or benign as its proponents claimed. Lauded as a substantial improvement over variolation, which had perpetuated smallpox epidemics throughout the eighteenth century, vaccination was not without its own risks and problems. Smallpox among the vaccinated soon proved early claims of lifelong immunity wrong. Yet people generally did not get vaccinated more than once because they worried that it might induce dangerous diseases or blood poisoning. Even normal vaccination might produce severe discomfort and temporary disability that made it difficult for adults to work. Vaccination also changed a lot over the course of its first one hundred years, as physicians tinkered with various sources for vaccine lymph and tried out all sorts of techniques and instruments.

To make matters worse, every innovation intended to resolve one problem just resulted in other complications. First physicians only reluctantly recognized that arm-to-arm vaccinations could transmit syphilis. Bovine lymph supposedly resolved this issue only to bring new organisms into play. Instead of syphilis, now blood poisoning and infections began to plague a significant number of vaccinations by the 1880s. The addition of the mild antiseptic glycerine supposedly resolved these problems, but lack of effective control over production, storage, and marketing of lymph led to widespread failure and complications from contaminated or outdated batches in 1901 and 1902.