Mattias Gardell writes that Koestler's thesis is "partly based on amateur anthropology",[3] and its scientific arguments come from The Myth of a Jewish Race (1975) by Raphael Patai and his daughter Jennifer.

[10] Writing in The Wall Street Journal, Chronicle of Higher Education editor Evan Goldstein states "Sand suggests that those who attacked Koestler's book did so not because it lacked merit, but because the critics were cowards and ideologues.

[13] Koestler did not see alleged Khazar ancestry as diminishing the claim of Jews to Israel, which he felt was based on the United Nations mandate and not on Biblical covenants or genetic inheritance.

[3][15] According to Jeffrey Kaplan, The Thirteenth Tribe was "Identity's primary source for the Khazar theory"; they felt Koestler's book confirmed their own beliefs regarding Jews,[14][16] and sold it "through their mail order services".

"[18] Reviewing the work in the Washington Report on Middle East Affairs in 1991, journalist and author Grace Halsell described it as a "carefully researched book" that "refutes the idea of a Jewish 'race'.

"[19] Despite some positive reviews in the press, James A. Beverley writes "When The Thirteenth Tribe was released, the academic critique of its research was prompt, public, and generally negative",[20] and Evan Goldstein states that it was "savaged by critics".

[23][24] Barkun describes the book as an "eccentric work", and writes that Koestler was "unequipped with the specialist background the subject might be thought to require", but that he "nevertheless made an amateur's serious attempt to investigate and support the theory.

[25] A 2005 study by Nebel et al., based on Y chromosome polymorphic markers, showed that Ashkenazi Jews are more closely related to other Jewish and Middle Eastern groups than to the populations among whom they lived in Europe.

They conclude: "However, if the R-M17 chromosomes in Ashkenazi Jews do indeed represent the vestiges of the mysterious Khazars then, according to our data, this contribution was limited to either a single founder or a few closely related men, and does not exceed ~ 12% of the present-day Ashkenazim".

[29] Writing in Science, Michael Balter states Koestler's thesis "clash[es] with several recent studies suggesting that Jewishness, including the Ashkenazi version, has deep genetic roots."