Case study. Can' put the finger on the issue... hmm. Website: abc.com On page SEO: done. Off page SEO: over 120 domains with do follow links (nofollow links excluded). PR 0-6, with various placement (sitewide and one page only, placement in footer, sidebar and contextual, keyword targeted anchor and non keyword targeted anchor, -> "natural" link scheme) Rankings: over 12 kw's in top 3 (competitiveness and kw search volume undisclosed). Niche: undisclosed. Problem: GWT indexed do follow backlinks: 9 domains (history of indexed links unknown: for my shame I didn't bother having a history of GWT backlinks of this client). Opensiteexplorer.org indexed do follow backlinks: 115 domains. Linkscape SEO Spyglass indexed do follow backlinks: 133 domains. Difference: over 90% less links indexed by Google. Reason: 1) As we all know, in GWT, Google doesn't show all the links/linking domains a website receives (they take them in consideration tho). That usually results in differences of backlink checking tools. That could be an explanation for this issue. However, in all my SEO career I have never seen over 90% difference in the backlink reports GWT vs. whatever tool. Most I've seen was in the 30-40% range. 2) I've heard rumors that the GWT disavow tool is working in an automated mode, disavowing blacklinks it finds unnatural. It could be a possible explanation but I can't confirm or infirm that statement. I've heard of similar cases some other SEO's faced in the last couple of weeks. I can't confirm or infirm this statement. Does anybody have different reasons about this? Any ideas?