Many web sites have portions of their site configured to use SSL. This allows the transfer of information between the server and the browser to take place over an encrypted connection.
URLs of such pages begin with https rather than http to indicate the secure protocol.
You may experience serious canonicalization problems if the secure portions of your site have been fully indexed along with your standard site.
Check the tutorial Search Engine Indexing of Secure Pages, to see how you can get around with that.