When I go through a Netherportal I get an half heart damage. Sometimes I get stuck in a wall or in the floor, too. The portal stands directly at a wall.
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I confirm this too. It's suffocation damage.
In the beginning I thought it was because at the other end the portal was built between walls in a corridor. But it is not because it also happens when the portal is built in spacious spots. In SMP I always receive half heart suffocation damage.
I can confirm this, i got a netherportal surrounded by stone left right top and bottom (front and back are free) and i get o.5 damage every time i go trough and i sometimes get stuck in the wall!

This still happens in 1.4.5, to me, but inconsistently: some portals do me damage, others don't.
For instance the one that damages me, that I know of:
nether portal at x:-2020 y:113 z:-208/-207, linked to overworld at x:-16162 y:48 z:-1662/-1663
Ones that do not:
nether portal at x:-2048 y:120 z:-222/-223, linked to overworld at x:-16380/-16381 y:77 z:-1776
nether portal at x:-2049 y:120 z:-166/-167, linked to overworld at x:-16389/-16390 y:57 z:-1337
(y values are foot position when standing in the portal)
None of these are against walls except the first overworld portal. No nether portal faces a wall.
(No idea if it's related to coordinates, but since certain portals always damage me, and certain portals never do, I figured hey.)

The portals that used to damage me, don't anymore as of 1.4.7. Anybody else?

Seems to be fixed in 1.4.7
No, not fixed. See this. (13w04a)
I can confirm this as well in the 1.5 release. I tried is in SSP and SMP.
SSP: Damage seems to only take place when you ENTER the nether, not when leaving it.
SMP: Damage is taken BOTH directions (entering AND exiting the Nether.)

Confirmed in 13w37b
still in 13w41b
I only took damage coming back to the Overworld from the Nether, I sometimes took 1/2 heart, sometimes 1 heart, and I heard the damage sound while in the 'loading terrain' screen.
I'm experiencing this in 1.7.2.
So far it's only occurred when I'm going from the Overworld to the Nether.

Is this still a concern in the latest Minecraft version 14w03b? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

This ticket is incomplete without the requested information, no response has been received within a reasonable time and we are assuming the issue has been resolved. If you are still experiencing this issue, we can reopen it at your request.
Please review the guidelines before reporting issues.

Could I ask, why this was not marked as fixed, if no one has been able to reproduce it lately? I'm a little unclear how it could be all of a sudden incomplete after more than a year of being an open confirmed issue.
I'll vouch that I could not reproduce this in 1.7.5. With the caveat that this bug was always tricky to make happen anyway.

We close tickets when people don't reply after about 45 days (to a request, for example I asked if it was still an issue, and got no reply), to reduce the number of tickets. We are more than willing to reopen a ticket at any time, if it is still occurring.
@sealbudsman, I think the difference between 'fixed' and 'incomplete' would be whether a programmer said, 'Oh, this is why that happened. I'll make and test something to correct it.' If we don't know why it started happening, and don't know why it stopped happening, it might start again. That's incomplete, not fixed.

Thanks for your responses, Ezekiel, Jaqi. It sounds good to me.
This bug is now present in 1.8-pre3 since dinnerbone fixed MC-3. I tested my portal created in a snapshot prior to the 1.8 release, and I now take damage after I get to the nether, depending on which of the two blocks I stand in when entering from the overworld.
Things to note: Prior to the fix for MC-3 when entering the other dimension when using a portal, you would still be in the portal, now you are no longer in the portal. I believe that this is the source of the damage bug as the player placement is now outside the portal and sometimes this might be inside a block. This could be fatal for the first trip to the nether if you're over lava so I really hope this bug gets escalated!
Both portals are facing north-south. When I enter the overworld portal standing on the left side while facing south, I exit the nether portal on the left side but one block over and forward, facing north. If I enter the overworld portal standing on the right side while facing south, I exit the nether on the left side, but TWO blocks over and forward, which for this portal was a wall so I took damage. My portals are the traditional size of 5 tall by 4 wide with the interior of the portal being 3 tall by 2 wide.
And here is some more information - One of my portals in the nether had the four blocks immediately in front of the portal (at the same level as you would be standing on the obsidian of the portal floor) filled with a half slab, which means before this breakage, you would exit the portal and then rise up a half slab height. After the bug was introduced, you now go somewhere else, which in my case is below the portal and into the lava pool underneath 😞

@@unknown: This is MC-73504
This is happening for me in the linux version of the latest snapshot (15w42a). It only happens on linux (I've tried mac and windows also) and only when leaving the nether on one of my portals. I take between 1 and 5 hearts of damage. Let me know if I need to create this as a separate bug.
@unknown: This is most likely a separate issue. If you can recreate it in a world created in 15w42a, please create a new ticket.
I came here to create a bug for this. It was happening on every teleport for me, both into and out of nether. I had created the portal completely embedded in rock except for one half of one face.