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I am using Google Custom Search on my site, if I set pages to "noindex" or "nofollow", does it also affect the custom search results on my site?

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Yes. Google Custom Search uses the indexed pages in Google, usually filtered for your domain. If you do not index your pages (noindex) CSE can't return them as a result.

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I tried to add noindex to some pages, but one week later, I still got those page from CSE result... – RRN Aug 7 '12 at 12:37
There is no fixed timeset for how long it will take for existing links to be removed. – pritaeas Aug 8 '12 at 8:05

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