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Why you might have a low click through rate CTR ..

Here are some reasons :

1-Untargeted traffic : is the major reason ..you might get visitors who are not looking for your content, this may be due to bad choice of your keywords.
solution : wise choice of keywords , genuine content , useful content

2-High number of pages : you must know that adsense impressions doesn't depend on unique visitors, it depends on page views.. so you might have 20 pages and have 20 visitors / day so you get impressions of 400 while there is only 20 people visited your site and about 2 clicked your ads
so your CTR will be 0,5 % which you will see as very low
solution : if this is the only reason , don't change it .. high number of pages is good and increase your alexa rank..keep it genuine and keep up the good work

3-Bad presentations : now most websites use adsense ..as a visitor, imagine how boring it will be that most sites have the same shape of advertisements
solution : try unusual forms of adsense as link ads..


4-Bad placing : most sites put ads at header or at the top..it is really good..but better is embedding in the content and link ads under the site link list ..most people recommend the large rectangle , but why don't you go for the button or half banner the are not used a lot and they appear attractive for me
solution : try embedding in your content..and embed small ad formats don't place a large rectangle in small width article .. don't annoy your reader.

5-Having so much adsense in a single page
solution : remove some ads dude..