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I have always been under the impression that the mosque on the Har HaBayis is on the location of the Kosdesh HaKodoshim. Is that accurate?

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I have never heard anyone say it was under the only mosque on the mountain. – Double AA Apr 27 '12 at 6:13

The Radva"z in responsum 691* confirms that without a doubt the אבן שתיה (and by extension, the inner sanctum) is located "under the dome". He also notes that figuring out the particulars of what used to be where on the Har Habayis is very tricky business and requires careful calculation.

*Bonus - This may also be the year construction on the dome was completed.

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Probably worth clarifying that this would mean that it was not where the mosque (Al Aqsa) is, but rather by the Dome of the Rock, which is not a mosque, since this is a common source of confusion (which is presumably what @DoubleAA is driving at in his comment on the question). – Loewian Dec 23 '15 at 16:01

That said, there are modern researchers who think that it was either (a) the base of the Mizbeyach (Altar), or (b) outside of the Temple complex altogether - according to this view, the sanctified part of the Har Habayis (500x500 cubits, Middos 2:1) lay in the southern half of the present-day Temple Mount (and incidentally, according to this view, the Kodesh Hakodashim turns out to be pretty much directly behind the Kosel plaza).

This was discussed in Techumin sometime in the '90s, although I'll have to look up the exact reference.

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Rav Moshe Sternbuch in his Shaalos U'Tshuvos writes that he is certain that the location of the mosque is not the exact location of the Kodshei HaKodoshim.

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do you know which volume and which teshuva? – Menachem Oct 3 '11 at 5:31

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