Google can identify the majority of affiliate links so they do not count as PageRank passing links. Affiliate links from the big providers, such as Doubleclick & Tradedoubler, should not show up in the link graph and therefore shouldn’t be something you need to worry about.
Typical affiliate links look like this,
The problem with custom affiliate schemes
The problem with affiliate links for search engines mainly occurs when you may have private or custom affiliate schemes, where the search engines don’t understand that they are affiliate links.
Typically these links will have been placed with commercial anchor text, but with no knowing intention to manipulate search engine rankings positions. Unfortunately these links can often be viewed as just that, manipulative keyword rich anchor text links, by search engines.
An example of a custom affiliate program
This is a custom affiliate program using obvious affiliate names in the URL and parameters. Search engines should be able to identify the nature of the link from this indications, but in many cases them maybe more obscure.
You should be very wary of removing private affiliate links, as they could be driving sales and revenue to your website. These links should all be marked as nofollow by the webmaster on the referring website.
In addition you should add these links to Disavow file at URL level. This can be problematic if there are many links of these links on a website. In this instance it is recommended that you Disavow the entire domain.
Below is an example of an article on the popular site Lifehacker.com. This page ranks well for terms around hosting and obviously gets traffic. This is a followed custom affiliate link, there could other links on the site which were naturally given freely in editorial, thus within the Google guidelines, therefore in this instance it would be recommended to nofollow the link (if possible) and disavow the link at URL level.
Affiliate scheme action
To ensure that future affiliate links that are built into your website are not seen as manipulative by Google, your affiliate scheme link generator should be updated to ensure these links add rel=”nofollow” by default.