This issue is a bit controversial. In the past, many MD/PhD or research oriented MD folks would do AP only or CP only which shaved off a year or two off residency training. Then they would jump into a lab where they would do a post-doc and then apply for tenure-track junior faculty positions in academic pathology departments.
Nowadays, whether one should do AP only/CP only or combined AP/CP is becoming a bit blurred. During interviews this past year, I've come across folks who agree with me that AP only is the right thing for me to do whereas others have commented that I'm making a mistake by not doing AP/CP. It seems that the pro-AP/CP camp are pushing even MD/PhDs to do AP/CP. Three reasons jump to mind:
First and foremost, AP/CP training provides a wider "safety net" for those who decide later on that they don't want to do research anymore (whether it be change of heart or just bad luck during postdoc years).
Second, pathology is changing in that the molecular diagnostics area of pathology is gaining momentum and is advancing fast. The days where diagnoses are made by just simply looking at frozens and H&E's may be fading. There is increasing infusion of molecular techniques in aiding the pathologist in analyzing tissues. Quick example...the increasing use of "special stains". Molecular diagnostics has paved the way for a lot of this. In any case, whether molecular diagnostics will be headed by CP or AP folks or both in the future is a bit uncertain. Some people predict that this will give rise to turf battles in the future...and that AP/CP certified folks will be immune to this because heck, they can do both, right? Furthermore, molecular diagnostics is a hotbed for pathology research right now.
Third, there is the "it's just one more year" which is a legitimate argument. AP or CP only can be done in 2.5-3 years. At most places it's 3 years for credentialling purposes but at other places, the rules are slightly bent. For AP/CP, residency will definitely be 4 years.
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Now, let's take a 180 degree turn and look at AP only or CP only. It seems that if you choose this option, you pretty much are confined to the academic arena. But it has been this way, it seems, for quite some time. The private practice sector seemed to be better suited for AP/CP folks since in that arena, you need folks who can do a little bit of everything.
But let's say you're going to run a lab 90-99% of the time and just dabble in the clinical side of pathology. Do you need both? Are you going to be using the skillsets for both AP or CP (the skillsets seem to be quite different in the AP realm vs. CP realm)? Many people still argue "no."
So whether you do combined AP/CP or AP only/CP only may depend on how committed you are to a certain career goal. Perhaps you can start by asking yourself this question (and be honest with yourself):
Are you going into pathology mainly because you want to be a pathologist or a researcher?
If you have a significant inkling of interest in being a pathologist, in addition to being a researcher, I would consider doing combined AP/CP.
If you see pathology as a means to equip yourself with additional knowledge and tools to help you eventually do disease-based research in the end and you see your ideal career as doing 100% bench research...then do AP only or CP only.