The complex, multilayered contact between the Quechuan and Aymaran languages is a central but still poorly understood issue in Andean prehistory. This paper proposes a periodization of that relationship and characterizes some aspects of the languages as they might have existed prior to their first contact. After disentangling the linguistic lineages on the basis of a large corpus of lexical data, the paper makes some observations about the phonology of Pre-Proto-Aymara: first, about aspiration and glottalization; second, about the glottal fricative *h; and third, about the phonotactic structure of lexical roots. The paper also presents lexical reconstructions of Proto-Aymara and Proto-Quechua and proposes provenances for several hundred roots. More than a third of the reconstructed Proto-Aymara lexicon may originate in Proto-Quechua. A method like the one presented here is a prerequisite for testing a hypothesis of genetic relatedness between the two families (and others in the region).