I'm really interested how many are out there.

Does anyone know any more?

シシャモ
トナカイ
神
ラッコ
オットセイ
サンベ
アイヌ
ユーカラ
ニポポ
コロボックル
コタン
ニシパ
ノンノ　
ルイベ
ケイマフリ
エトピリカ
ハスカップ
ホッキ貝
コマイ　(氷下魚)

I'll be editing the list to put those that people find.

Perhaps not quite what you're looking for, but it seems like about half the place names in Hokkaido are Ainu.

I've got a book at home that I picked up at an Ainu museum/village a while back. I seem to recall if had a short glossary in the back consisting of a few pages of words in Ainu translated into Japanese and English, though it was far from being a dictionary. It may have contained a list of Ainu loanwords as well, it's been a while since I read it. I'll have to dig it out when I get back home and check.

Yes, I know they are. It only makes sense. Some things are hard to pinpoint as Ainu words without prior knowledge of both languages. I believe reading that 熊 was also a loan. Also, I believe ケセン語 has heavy influence. I believe the word 蝦夷, either read as ezo or emishi comes from Ainu. I'm sure there are some native words that are actually from Ainu but it's just hard to tell. I just want to know of more than what's on the Japanese Wikipedia page.

Found this: http://www.asahi-net.or.jp/~hi5k-stu/aynu/nihongo.htm

I'll keep digging...

Dug out the book. It didn't list any loanwords, though there was a list of place names in Hokkaido that are derived from Ainu, along with their meaning.