A secondary is the second part of the medical school application. The primary application is the first, very general "this is who I am" application. Every school recieves the exact same primary from you.
The secondary is sent out by individual medical schools and is usually more greared towards what that particular school wants to know about you. Sometimes it asks "Why our school?" etc. Secondaries get sent out to you only after the primary application is received.
Most schools send them out automatically once your primary app is processed. It consists of a couple more essay prompts that are unique to each school. They are supposed to help schools weed out who they want to interview, but really it's a way for schools to make money (each one costs about $100 a pop these days ).