Polyether ether ketone (PEEK) is a promising material for the encapsulation of electronic components for medical implants but a strong and hermetic joining technology is required. Autohesion is a self-bonding method that avoids the need for adhesives. The strengths of autohesive joins using amorphous and semi-crystalline PEEK films after surface activation using RF plasma were compared. Both types of PEEK films showed successful autohesion after activation with the bond strength of the amorphous sample being twice as high as the bond strength of the semi-crystalline sample. Plasma treatment increased the autohesion strength of PEEK with no observed change in surface roughness (as measured by profilometer). The water contact angle was reduced by the treatment. X-ray photoelectron spectroscopy (XPS) was carried out to determine surface chemistry. In the case of the semi-crystalline surface, plasma treatment increased the relative percentage of CO functional groups compared to the untreated surface. For treated surfaces nitrogen concentration correlated positively with bond strength while oxygen concentration correlated negatively with the semi-crystalline PEEK samples and positively with the amorphous PEEK samples. The oxygen groups most likely are formed after the treatment by ambient oxidation are not conducive to bond formation, possibly because of the quenching of radicals that would otherwise form links. Copyright © 2010 John Wiley & Sons, Ltd.