In 1986, Starostin and Igor M. Diakonoff suggested that the Hurro-Urartian languages belong to the Northeast Caucasian language family. Starostin was also instrumental in the reconstruction of Proto-Kiranti, Proto-Tibeto-Burman, Proto-Yeniseian, Proto-North-Caucasian, and Proto-Altaic. He developed the theory, originated by Abu al-Ghazi Bahadur Khan in the 17th century, but really revived by Gustaf John Ramstedt in the early 20th century, that Japanese is an Altaic language.
The Dené–Caucasian hypothesis proposes that Northwest Caucasian, Northeast Caucasian, Yeniseian, Sino-Tibetan, and Na-Dené form a single, higher-order language family. According to Starostin, the Dené–Caucasian and Austric macrofamilies, together with the Nostratic macrofamily (as envisaged by Vladislav Illich-Svitych, with some modifications), can further be linked at an earlier stage, which Starostin called the Borean (i.e. 'Northern') languages.
Since 1985, Starostin had been developing STARLING a linguist's workplace software. He was assisted in his work by Murray Gell-Mann, a Nobel Prize-winning physicist. At the time of his death, he was a professor at the Russian State University for the Humanities, a visiting professor at the Santa Fe Institute, and a frequent guest lecturer at Leiden University in the Netherlands, where he was awarded the degree of Doctor honoris causa in June 2005.