The Jesuit missionary Alessandro Valignano, praised for adapting Christianity to the cultures of Japan and China, did not support a similar strategy for India and Africa. He theorized racial hierarchies in which a darker skin was associated with ignorance and vice, whereas the similarity to European physical features implied a higher degree of civilisation. Numerous and sincere conversions could be expected in East Asia, whereas the Indian and African neophytes were allegedly led only by terrestrial concerns. A tabula rasa policy was wished so as to transform the “black” new Christians into Europeans. The “Valignano hypothesis” suggests that the close association of accommodatio with racial hierarchies was due to concrete political and economic contexts. The Africans and Indians that converted to Christianity were mostly colonial subjects or tributaries, whereas in the East Asian polities the conversions were not accompanied by any effective Portuguese coercion. As the Thomas Christians of South India were neither subjects or commodities of the Portuguese, Valignano evaluated them in a way closer to the East Asians than to the Indians in general. In 1606, when Valignano died, Roberto Nobili started an accommodationist mission in Madurai, outside the reach of the Portuguese and in a vibrant cultural center ruled by a powerful local dynasty. A clear continuity linked Valignano and Nobili. While they had different evaluations of which society were civilised, they agreed on the racial, political and economic justification of accomodatio. The Badaga caste, to which the local rulers belonged, was differentiated from “the other dark people” and perceived as not inferior to the Japanese, hence it deserved accommodatio together with the Brahmanical elites. Through the ‘Valignano hypothesis’ we realize the anachronism affecting all analogies between the early modern hierarchical accommodatio and post-Vatican II Catholic efforts towards inculturation.