This article includes asmall  list of Scottish Gaelic words of possible non-Indo-European origin. This article will likely contain fewer words than originally planned and only some of the possible pre IE words I have found. Note that this article was originally titled: 27: General non-IE Gaelic vocabulary, (long article, being updated). Note that this section does not include a large number of or even many of the Gaelic cognates I have published about on the ebooks available on this site and in other books. This is in fact a very small but interesting list and I have discussed far more examples elsewhere, a great number of them. Below are the ones published here:

1). Giogh- as in the island names Giogha and Gioghaigh - possibly related to Icelandic gjá and Gaelic geodha and Manx ghaw in place-names, and Orkney Scots geo, but this does not quite make sense I think as there are not that many "geos" on either island, so instead I wonder if these island names connect to a female goddess entity, in which case there might be a connection with the word Sheela-na-Gig, where the "Gig" element is not fully understood etymologically, but where there is an obvious connection to female goddess figures. I also think that the root word present in these words could be connected to Icelandic gýgr referring to a giantess, compare also Orkney Norn: gýro and Norwegian gyger. 

2). athach - "giant" or "monster". This word can also mean "a peasant" however. The word athach can also mean a gust of wind, which is interesting.
3). Fadhail - "ford", lends its name to the island of Benbecula, related to Germanic and Latin words and to English "wade", but likely I think of non-Indo-European origin.
4). oro- as in the names Oronsay and Orosay, perhaps connected to Uralic *ura - groove or channel, which may make sense given the way that both Oronsay and Orosay and separated from the mainland by shallow channels. 

5). ciuthach - another form of giant or aquatic ancestor. Related to Manx Cughtagh. I have written about these ancestors quite a lot before, because there are some really interesting things pertaining to them and to the prehistoric peoples of Western Scotland. I would like to mention in this article specifically though something pertaining to them and the folklore of Yorkshire.

6). giosagach - magical, unknown etymology

7). pruchlais - den or cave, according to Am Faclair Beag ( faclair.com ). This word is likely related to brugh - "broch", although the formation of the word pruchlais may imply other information coded into the word's syllables. 

8). ròig - den or cave, according to Am Faclair Beag ( faclair.com ). Unknown etymology. Possibly related to Finnish rotko - "chasm", "ravine" or "gully". 

9). sgailp - den or cave, according to Am Faclair Beag ( faclair.com ). Unknown etymology. Perhaps connected to Orkney Scots gloup for a geo-like coastal feature, and perhaps related to English "gulp" as in to swallow.  

10). cuta - a short log (1)

(1): A pronouncing and etymological dictionary of the Gaelic language, by Malcomb MacLennan

I hope that this article was an interesting read. I will be writing much more on yet more Scottish Gaelic vocabulary in the future. This article is dedicated to my cat and to the ancestors of Scotland, and to my grandad.