After eight years of studies, Aguinaga graduated from the Universidad Nacional Federico Villarreal in Lima with a medical degree, in 1975. From 1977 to 1979, he furthered his qualification at the National University of San Marcos, specialising in general and digestive system surgery. From 1981 to 1985, he attended a post-gradual training in gastrointestinal surgery at the Louis Pasteur University in Strasbourg, France. From 1985 to 2006 he practiced at the Archbishop Loayza Hospital in Lima, starting as an assistant surgeon and later gaining promotion to general director. As a professor, he has lectured about surgery at the Cayetano Heredia University, the Universidad de San Martín de Porres, and the private University San Juan Bautista. Additionally, he became the personal doctor of president Alberto Fujimori.
In Fujimori's administration, he held the post of vice minister of health from 1994 to 1999 and eventually he became minister heading the same ministry from 1999 to 2000. In 2006, Aguinaga was elected to the Congress on the Fujimorist Alliance for the Future list. In 2011, he was re-elected for another five-year term for the Fuerza 2011 party of Fujimori's daughter Keiko.
While Aguinaga was Minister of Health there were taken place forced sterilizations, specially to indigenous people.
- "Ficha de Congresista". Congreso de la Republica del Peru. Retrieved 29 December 2010.
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- Official Congressional Site (2006 term)
- Congressional site (2011 term)
- Resume on the National Electoral Panel (JNE) site
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