Abstract Glycogen debranching enzyme (GDE) is together with glycogen phosphorylase responsible for the degradation of glycogen. The present study compares the post-mortem activity of GDE and breakdown of the glycogen pools in M. longissimus dorsi of RN − carrier pigs and in wild type animals. The activity of GDE ( n = 14) and pH ( n = 20) was measured 0.5, 3, 5, 24 and 48 h post-mortem. The change in pro-glycogen and in macro-glycogen content ( n = 20) was followed until 216 h post-mortem and the transcription level of GDE, glycogenin and glycogen synthase m-RNA ( n = 19) were measured 0.5 h post-mortem. Both the activity of GDE and the transcription level of GDE were found to be similar in RN − carriers and wild type animals shortly after slaughter. However, the activity declined faster in wild type animals compared with RN − carriers with increasing time post-mortem. The contents of both pro-glycogen and macro-glycogen were higher in RN − carriers compared with wild type animals, and further, the proportion of macro-glycogen was higher in RN − carriers compared with wild type animals. During the post-mortem period, only degradation of pro-glycogen was observed in both genotypes. The decrease in pH was faster and the ultimate pH lower in RN − carriers than in wild type animals. It was suggested that the higher GDE activity in the late phase of the post-mortem period in muscles from RN − carriers renders the extended pH decrease in these muscles.