In 1968, thanks to a postdoctoral fellowship from the Wenner-Gren Foundation, he traveled to South Africa to study early hominid fossils and to Kenya to excavate in the Tugen Hills with the archaeologist Louis Leakey.

[6] In the early years of his professional career in the 1950s, Aguirre promoted conferences, meetings, and scientific publications at a time when the national Catholicism of Francisco Franco's regime hindered the dissemination of Charles Darwin's theory.

[4] In 1962, Aguirre published his lecture "Paleontological problems and natural selection",[7] in which he stated his defense of the modern synthetic theory of evolution, as opposed to the theistic dirigiste approaches commonly adopted at the time.

The work was co-directed by the paleontologists Miguel Crusafont, Bermudo Meléndez [es], and Aguirre, and included articles that covered biological evolution from very different approaches, including Crusafont's orthogenetic dirigiste ideas, but above all, it exposed the synthetic theory, assumed by most of the authors, among whom, besides Aguirre, were Ramón Margalef, Antonio Prevosti, Salustio and Rafael Alvarado, Francisco Bernis or José Antonio Valverde.

[4] Being the first paleontologist to decipher the importance of the archaeological site, Aguirre became its first director in 1978 and remained in this post until 1990, when he resigned and José María Bermúdez de Castro, Juan Luis Arsuaga and Eudald Carbonell took over the role.