I found that a workaround for this issue is to add the following to my Xresources: XTerm.vt100.scaleHeight: 0.9 The default is 1.0 (which creates the problem), a value of 1.5 also makes it work (although fonts look too wide then). I found this information here: https://savannah.nongnu.org/bugs/index.php?52165 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=880407 Which might indicate this being a freetype problem?