His left eye is clearly out of alignment vertically; I’ve known folks with eyes out of line on the horizontal axis, but never this.
Did it give him any particular difficulty?
Looks to me like a badly lit photograph, causing a shadow around his eyes.
Maybe he’s Emmanuelle Vaugier’s great-great-grandfather.
Long exposure. The other eye was stronger so he favored it 'cuz he didn’t want to look like a dork in glasses. Lotsa reasons.
His face isn’t symmetrical. One side is larger than the other. This is actually fairly common. In Lincoln’s case, it could be due to something like Bell’s Palsy, because it looks like it got more obvious as he got older. People with Bell’s Palsy have “droop” on one side of their face.
Also, it took a long time to expose a photo back then, and you had to sit still for a while; Lincoln may not have had his eyes focused on anything.
My God, his ears don’t line up either!
Actually, he head is just cocked to one side. If you rotate the picture 4 degrees, his eyes and ears are aligned.
If you rotate your head 4 degrees upward, you might see the joke that just went over it.
I understood the joke. That’s exactly what I was commenting on. You’re the one that was whooshed. 
I don’t think it’s that uncommon. Our local weather man’s eyes are further out of alignment than that, for example.
Can you let the rest of us in on it, please? 
I’d be interested as well.
My eyes are slightly out of alignment as well. I can’t recall which eye is higher than the other, because in my case it’s not enough to notice unless you really try hard, but it does have a minor impact. I cannot see those ‘3-D’ pictures where you need to let your eyes cross, because mine don’t cross ‘evenly’.
I didn’t discover the ‘problem’ until I was 40-something when I went to my eye doctor with eye strain; he gave me a prescription for glasses that have s prism in one lens to shift the image up (or possibly down, I don’t recall) so that both eyes would see images on the same plane.
They didn’t really help with the eye strain though. But I fixed that by taking more frequent breaks from starting at my computer screen at work. I stopped wearing the glasses after a while; i think my body had just gotten used to the way my eyes operated, and trying to change out after first years just want working.
It’s pretty obvious. The apparent misalignment is due to Lincoln’s head being slightly cocked to one side (as the misaligned ears also indicate, as Speedway Ryan also noticed, but chose not to explain). In other photos, his eyes and the tops of his ears are more aligned. His eyes are somewhat asymmetric, but I don’t think they are at greatly different levels.
I don’t think you could demonstrate lack of alignment of the eyes from a photograph unless you were sure his head was exactly level.
But if you rotate the photo until it’s level . . . then his mouth is crooked.
The problem, though is with his eyebrows. They seem to extend downward, all the way to his eyes.
All joking aside, everyone has a certain amount of facial asymmetry. Wikipedia even has a nice drawing of a face that has been cut in half and each half duplicated and flipped to make the point.
See the picture at the top of this article:
That said, Lincoln’s face showed a greater degree of asymmetry than what is normal.
Cite:
Many of the potential implications of Lincoln’s facial asymmetry along with his other distinctive features are discussed at length in this wikipedia article:
Obviously, any human being with two functional eyes can make them line up parallel to the ground any time they like.
Whether your ears, eyebrows and mouth will be getting with the program at the same time is a whole 'nother matter. But ears, eyebrows and mouth make no contribution to vision. So I don’t see how any “misalignment” could make a difference
More concerning to me is his nose. I never realized before that he had three nostrils.
He’s got Bette Davis eyes.