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I was planning on using Atlas Code 100 track .....
I'm going code 100 because this is for my son (4 years old) and it is my understanding that some engines/cars can have problems with code 83. Probably nothing I will end up buying for him, but better safe than sorry is my motto.
I'm a newbie though. Is there a reason in terms of functionality only that one should be used over the other?
No, both code 83 and code 100 track function the same. There is almost no equipment that's not over 20 years old that will not run on code 83 track. The only reason to use code 83 track is that is close to (but still larger than) typical 125 pound mainline rail. Code 100 track is generally cheaper so that may also be a consideration. If money's not an issue, I would use code 83 assuming that your son's layout may someday, just by chance, become your model railroad.

Really the only reason that some modelers use code 83 and others use code 100 is personal preference. I work with code 100 myself.
What is the technical difference between code 83 and 100? I thought 100 was slightly taller.
If it is Atlas, they made the ties on the shorter Code 83 taller than those used on their Code 100 so that the two can be matched in height that way. You still need the transition joiners, though, which are a pain where the Sun don't shine. You will have to use a small metal file to bevel all the mating ends of each rail or your transition joiners will bend and not slide into place. At least, the ones I got were like that.
Code 100 means 100/1000ths of an inch from rail foot to the top of the head. Code 83 is 17/1000ths shorter. (100 - 83 = 17)
As Selector said, its just a height thing, code 83 (.083") better represents 132-140lbs rail in HO scale, where as code 100 (.100") represents somewhere in the range of 155+ lbs rail (which is real, but rare in the US).
Code 100 is huge for the scale. In the real world, that translates to 150lbs+ which is only used on Amtrak's Northeast Corridor. Code 83 is also huge..even for mainlines. However, 83 is the most accurate for simulating Class I mainline, as Code 70 is more for branchline/shortline mainlines (or spurs for Class I's).
On my newest layout I have been using Code 70 for tangents, Code 83 for curves (all jointed rail), Code 55 for sidings, and Code 40 for industrial spurs. It looks great, and I haven't had any problems with cars not running on them.
Either way, for a first layout I would stick with Code 100. It is easy to work with, plus there are tons of different pieces available (not to mention it is the cheapest option!).
Boy, I'll bet that Code 40 looks great on the industrial spurs. Nothing harder than trying to make Code 100 track look overgrown and sunk in the mud.
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