What is the difference? Both seem to be bonds backed by mortgages.
Whole Loan A term used to distinguish between an original mortgage loan and a pass-through security. Notes: Whole loans are usually larger in size than the maximum amount allowed within GNMA, FNMA and, FHLMC’s standards. Private entities pool whole-loans together with credit enhancements to create whole loan CMOs. Credit enhancements ensure investors receive timely interest payments.
whole loan are kind of non-agency loans that were not sanctioned by the full-faith and credit of the governing organizations because their did not meet some criterias (size is one if the major decision factor - as correclty pointed out by Sanyaiz) Or for a complete detailed difference look at page-3 here on S&P http://www2.standardandpoors.com/spf/pdf/products/060605_whole_loan_salesSNAP.pdf