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In late 1902, in the midst of clashes with Oswaldo Cruz over the Federal Serum Therapy Institute’s policy on the production of sera and vaccines, the Baron of Pedro Afonso stepped down from his post. On December 9, Cruz was named to replace him as director-general.

Cruz had only just assumed his duties when he was invited to replace Nuno de Andrade as head of the General Directorate of Public Health, an agency subordinated to the Ministry of Justice and Internal Affairs. Among its duties was the coordination of sanitary services at Brazilian ports and research into infectious diseases.

Cruz was only 30 and basically unknown outside of medical circles. Nevertheless, when he was instated on March 23, 1903, he presented a thoroughgoing plan to eradicate yellow fever from Rio de Janeiro within three years at most. He also promised to vanquish two other maladies that often hit the nation’s capital in violent epidemic form: smallpox and the bubonic plague.

These sanitary campaigns were part of an even more ambitious urban reform project, known as the Pereira Passos Reform in reference to the engineer who led it, Francisco Pereira Passos, appointed mayor of the federal capital in 1903 by Brazilian President Rodrigues Alves.

Before he could implement these campaigns, Cruz first needed to validate himself. He soon drafted new sanitary legislation that would do away with the overlapping public health jurisdictions between the federal government and the mayor’s office in the federal capital. Approved by Congress in January 1904, the new law transferred control over all actions in the capital to the General Directorate of Public Health. Among its roles, the agency would now be responsible for defensive hygiene services, the sanitary police, the prevention of contagious diseases, and actions aimed at household hygiene.

Distrust and outright opposition notwithstanding, the campaigns against yellow fever and the bubonic plague were victorious. By 1904, Cruz could celebrate a sharp drop in morbidity and mortality rates from both illnesses, a trend that was to continue the following years. His endeavors in the realm of smallpox were not as successful. Based on mandatory vaccination, the smallpox campaign was attacked by the press and even medical circles, eventually culminating in the eruption of the Vaccine Revolt in 1904. Mandatory vaccination was suspended and four years later the capital was struck by yet another outbreak of the disease.

With the plague and yellow fever epidemics under control, Cruz could extend his public health actions elsewhere. In 1905 and 1906, he made two long expeditions to Brazil’s sea and river ports, resulting in a preliminary survey of sanitary conditions in various regions across Brazil’s vast territory.

Lauded for his triumphant leadership of the yellow fever campaign, Cruz stayed at the head of the General Directorate of Public Health under the Afonso Pena administration (1906-1909); it was then that he tried to make the fight against tuberculosis his new mission. But without the backing of the Executive branch, his plan could not move forward. So when a new law went into effect in November 1909, prohibiting anyone from holding more than one federal post, Cruz did not hesitate—he opted for his home, the one located on the former Manguinhos Farm, by then already renamed the Oswaldo Cruz Institute.