A junior mortgage is any mortgage subordinate to the primary mortgage. This commonly refers to a second mortgage but can also refer to a third or fourth mortgage or a home equity line of credit. When someone purchases a home, they may not be able to make a 20 percent down payment. They may take out a junior mortgage to make up the difference. Some take junior mortgages to consolidate bills into a single payment instead of multiple. The main difference between the primary and junior mortgage is the order of payment that happens when the property owner sells. The primary mortgage is always paid first. If there are enough funds after the first mortgage, any junior mortgage is paid. If there are not enough funds after paying the first mortgage, the property seller is obligated to pay the difference on the junior mortgages.