I got same problem with this : I have two profiles running off the same javascript tag, one that accepts all traffic (minus internal traffic that is filtered out), and one that just collects SEO traffic (done using a custom include filter where Campaign Medium is set to "organic"), minus the internal traffic as well. The search engine numbers theoretically should match between the two profiles. Take yesterday for example: SEO Profile All Traffic Profile ------------------ ------------------------- Google 3,954 3,904 Bing 1,222 1,211 Yahoo 885 899 Thoughts on why these would be different? Source: http://www.google.fm/support/forum/p/Google+Analytics/thread?tid=67541b13891c2bd6&hl=en