Caetano's contributions have been widely recognised and he is included in the list of Highly Cited Researchers (Thomson Reuters) and has won the BD Biosciences Prize of the European Macrophage and Dendritic Cell Society (2002), the Liliane Bettencourt for Life Sciences Award (2008), the Award for Excellence in Basic/Translational Research from the European Society for Clinical Investigation (2011) and the Louis-Jeantet Prize for Medicine (2017).
He is a fellow of the Royal Society (elected 2019), fellow of The Academy of Medical Sciences (elected 2006), a member of the European Molecular Biology Organisation (EMBO; elected 2006) and was made an Officer of the Order of Sant'Iago da Espada by the government of Portugal, his home country, in 2009.