The extruder on my Prusa i3 MK3S keeps clogging while printing. Loading is fine, and each time it clogs, unloading and loading the filament seems to work. The filament extruded just after resolving a clog looks like it has small bubbled on it.

The problem only seems to happen when printing certain models. Printing the Batman symbol at 0.15 mm works every time. But the model I'm trying to print always fails at most a few minutes in.

I've tried cleaning the nozzle. Cold pull twice, and taken it out and heated it with my airgun and trying to work on it with the acupuncture needle.

The print that fails is this "Small Pill Container" with 0.1 mm layer height and 100 % infill, but printing a simple cylinder shape (25 mm outer diameter, 2.5 mm walls) creates the same problem. Trying to print them both at the same slicer settings with 0.15 mm layer height still fails.

The model was sliced using the newest version of PrusaSlicer 2.1.0 and printed with Prusament PLA at the factory recommended 215±10 °C, and tried 220 °C.

Any ideas what could be happening? Anybody experienced a similar issue?

Printing the bundled TreeFrog 50 μm sliced by Prusa for the Prusa I3 MK3S cased the same problem. Jam happened about 30 min in. I guess this rules out slicer problems as the root cause.

After a lot of research, it seems a lot of people have problems with the MK3 clogging, especially with PLA, and especially with prints with a lot of retractions. The issue seems to be the design of the heat-break, which has a throat between 2.2 mm and 2 mm, where the PLA can get stuck. I've ordered a new heatbreak. Please read this answer of my findings.

  • $\begingroup$ Sounds like a retraction problem. Use less retraction. $\endgroup$
    – user77232
    Nov 14 '19 at 12:43
  • $\begingroup$ @user77232 The cura slice with 20% infill had the same retraction setting, and it's what I've been using for all the prints that succeeded as well, so I don't think that's the issue. Maybe it a combination of factor where retraction is one of them? $\endgroup$ Nov 14 '19 at 13:47
  • $\begingroup$ 215 to 220 °C for PLA is pretty high, try reducing the temperature to 195 to 200 °C. $\endgroup$
    – 0scar
    Nov 14 '19 at 14:28
  • $\begingroup$ Tried, but with the same settings it still clogged. Although, I'm now printing it with retraction completely disabled. Though not a permanent solution, as it ends up stringing quite a bit on the first few layers, it might point to the root problem? $\endgroup$ Nov 14 '19 at 15:06
  • 2
    $\begingroup$ Prusa Mk3 has a genuine all-metal hotend by e3d - which means it has all the all-metal problems, which means don't go overboard on retractions. $\endgroup$
    – Trish
    Nov 16 '19 at 17:20

My problem was 2 things. The heatbreak, which was switched out for the MK2 version(Explantation below). And the Teflon Tube that runs down the heatsink.


Change the heat-break to a generic E3D one. You can order the heatbreak for the MK2 from prusa, or any generic heat break for the E3D hot-end assembly.

On the Prusa i3 MK3(s), this component has been given a 45° taper in the middle, between 2.2 and 2 mm. This is done to ease filament retraction for the MMU, and will be nothing but problematic if you are not using the multi-material upgrade. Especially with higher nozzle pressures(eq. with lower layer lines), the filament may be squeezed into this taper, clogging the hot-end.

You may not experience full clogs, but partial ones that will show themselves as streaks in certain layers on the print.

Heatsink Teflon Tube

There is a teflon tube that runs down the heatsink. It's crucial that this is mounted correctly and it is not entirely intuative how.

First, press the teflon tube into the heatsink all the way to the bottom. Then, try to pull it out slightly. You'll notice that the small plastic ring at the top of the heatsink will pull out slightly along with it. Now, hold this black plastic part at it's current position with your fingernail, and push the teflon tube in the extra amount. When done, there should be no play in the tube.


The problem with low layer heights is that the filament flow is low, this means that the filament is at prolonged times at temperature, filament cooking can cause clogging. Try increasing the layer height to 0.2 mm to observe if the same clogging problems still occur, furthermore, try lowering the extrusion temperature.

Also, heat creep is a known issue (insufficient cooling of the cold end) to cause clogging. Note that this is unlikely on the Prusa MK3S, but you could check whether the fan rotates freely and that there are no additional obstructions in the flow path.

It could be that a combination of too much hotend temperature and a low filament flow is causing this issue.

  • $\begingroup$ I've tried setting the layer height to 0.15 mm, and the same problem occurred. Just for test I tried the batman logo at 30% speed, and it seems fine, so I'm inclined to belive that filament cooking is not the issue? Although I'll try it at 0.2 mm and report back to be sure. I checked for heat creep, but the fan is running smoothly at full speed, with no obstruction, and does not seem hot. $\endgroup$ Nov 14 '19 at 13:44
  • 1
    $\begingroup$ @SomeNorwegianGuy Indeed we can rule this out in this case, but it was a possibility. I'll leave the answer in case others may find this question. $\endgroup$
    – 0scar
    Nov 14 '19 at 14:16

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.