Ok i'm going to try to explain this as clearly as possible. I have a 2006 IS350 and the body right above the rear door sticks our differently on both sides of the vehicle. This is for the rear doors only not the front, right above the glass where it curves down towards the REAR of the vehicle. On my passenger side the body stick out over the glass part of the door a good 3/4 of an inch. On the drivers side it only sticks out above the door about 1/4 of an inch. It the body part right between the roof and door that encases the door itself. You can only notice it when both doors are closed. It looks to be some sort of manufacturing defect but i'm not sure. On the inside both doors looks the same and have the same amount of clearance. On the outside it apears that the passenger door is not flush to the body but rather sunk in about 1/2 an inch, this is only noticable on the top curvature of the glass as the body protrudes out much further above the glass than the drivers side, the rest of the door is aligned perfectly. I have a keen eye for things but can someone else check their vehicle to see if something similar is on their car. I thought that the glass part might be pushes in but it's fixed to the door, their is no movement or play. Not to mention both door close perfectly and below the glass are perfectly aligned.

Sounds like your door needs to be adjusted. I just looked at mine and it's all almost flush on both sides of the car. I ran my fingers between roof and doors and it's all the same.

Well that's the funny thing, it has nothing to do with the door being adjusted as the rest of the door aligns, if I pushed the door out the rest of the door would stick out from the body. I'll have to take some pictures so everyone can see what i'm talking about. Even the upper most metal part of the passsenger side door that protrudes out past the glass towards the rear is perfectly aligned. It just the window frame itself that looks like it's pushed in. I thought at first that the body might have shifted causing this problem. The car was in a minor front end accident before I bought it. However I made measurements on both side when the door wehere open and both sides are equal, it's the door itself that is casing the issue. Weird thing is that when the door is closed on the inside the door is not any tighter on the passenger side compared to the drivers side. I'm still leaning towards factory error but i really don't know.

Well there is some "sculpturing" and inset at the back of that window, but it's the same on both sides.

I went out and looked at mine, I see where your having your issue. 3/4 of an inch is alot! Mines flush on both sides. So I can see where your visually bothered by this. I would be to. So let me ask this, if you look down at an angle and try to see behind the edge of the door, is the amount of space about the same all the way down the door also? or does the edge of the door right there seem alot closer to the quarter panel? If it looks alot closer right there, then it's bent and can be fixed pretty easily by a body pro with some banging and bending. I would let them fix it, you don't wanna crack or chip your paint. It won't effect the door seal or fitment as this part of the door is more of an overhanging edge and the actual seal is well inside. I can easily see how this part of the door can be bent or pushed in without effecting any other part of the door. I don't see someone bending it 3/4 of an inch, but it looks to me like it could be from just using this area of the door to push on to close the door. Maybe as years went by and repeated use? But I think somehow this part of your door just got pushed in by something.

Well I really inspected everything on both sides. Both doors are identical so there is nothing wrong or bent in the door itself. Smooth1 to answer your question the clearance of the door on the passenger side is the same as the drivers side. If I look at an angle the amount of space is even across the door except it gets tighter uptop. One thing that clued me into the door being off is that the weather stripping is creased all around the top, the door seals fine and is easy to close but the weather seal is basically crushed meaning that after years of the door being out of alignment it put too much pressure on the weather stripping and permanently creased the seal. One thing I should also mention is the the front passenger door is also pushed more in compared to the drivers door, the weather stripping around the door is also showing creasing although not as bad as the rear door.

After further inspection comparing both sides of the car I found that the bottom of the passenger side doors seem to protrude out more compared to the drivers side. It's not much but it is noticable if you run your finger across the botton the door over the gap between the door and the sideskirt. The drivers side is flush or the door is recessed slightly back, on the passenger side the door is slightly overlapped. I'm now beginning to believe this has been a factory installation problem with the door itself. The question is how to I adjust the door the fix this? I was thinking of loosening 3 of the 4 bolts that hold the door on the hinge leaving all but the very bottom hinge bolt. I would then pull back on the door and and tighten it all back up. It just needs to rotate outwards on a horizontal axis. I may be exagerrating alittle when I said 3/4 of an inch. I did measure and the the door is recessed about 3/8 and inch away from the body where the drivers doors are only recessed less than an 1/8 inch away.

Smooth1 I also think your referring to a different part of the door than I am. All metal parts of the door are aligned except for the bottom where it seems to protrude out slightly more than the driver side. THe part that is noticable is the upper most part of the door above the glass where the body of the car or roof slightly overhang about 1/4 more on the passenger side compared the drivers side.

Man, post some pics.

Yeah i'll try when I get home later this evening.

I'm unable to picture the exact place you are talking about, but it does not sound normal.

I would highly recommend against adjusting the hinges yourself. Body panel and door alignment can be a major ordeal. If it were mine, I would take it to a body shop.

If you're bent on attempting it, be sure to have at least one friend help out. Doors are heavier than they look! You'll also likely need a breaker bar for the bolts (if you don't have access to an impact gun). Lastly, I would score a mark around the hinge so you can get the door back to its current condition. There is a good chance that you will find that the problem lies with the body panel instead. I've used a Sharpie if you don't wan to score it, although its not as "accurate".

Good luck with your decision.

Well there is no way it can be a body panel unless the entire car is out of whack. That side of the car has never been touched as far as an accident is concerned. The only accident that car was in was the front driverside which was a garage accident that was slow and only creased the hood and cracked the headlight housing. The body panel i'm referring to that is sticking out is on the passenger side roof rail on the other side of the drainage gutter. The is a fixed piece that is very solid. If that shifted outward then the entire roof would have shifted and that's not the case.

Need Pics Man !