I originally posted this reply in the DO applying for MD ortho thread.
"Traditionally in the past none of these programs were linked and they would take as many interns who were interested in getting a PGY2 spot. So what you would end up with is 8-10 interns competing for 2-3 PGY2 spots. Once they landed a PGY2, they finished out the remainder of the residency. Those that didn't land a spot were forced to pick a residency in a different specialty.
Now, about 4-5 years ago some of the less popular programs decided to link the internship with the residency, meaning that if you landed the internship you would go on to the PGY2 spot w/o fear of someone else taking it (basically the same as the MD programs). The reason that the less popular programs did this was to attract better candidates from the more popular programs. Over the next couple of years, this forced more programs to link b/c the quality of their applicants was going down. Currently, about 20 of the 29 programs are "linked" and every year more programs end up "linking".
Matching ortho, whether its allopathic or osteopathic, is a very difficult task b/c there are many more applicants than spots. The reality is that many people are turned away and have to choose another profession."
The only thing that I would add is that the programs that aren't linked only weed out the interns. Once you hit pgy2 there is no competition with other residents to make it to pgy3 and so forth. Hope this helps.