Skeletal muscle cell culture is an important tool to discover the pathogenesis of rare canine neuromuscular diseases. The aim of the current study was to improve an existing clinical protocol to extract and cultivate canine myoblasts by using different enzymes for tissue digestion. The contamination of the mixed culture with fibrocytes should be minimized, a higher number of myoblasts with a shorter lag period should be gained and the influence of transport length on the myoblast numbers should be assessed. Twenty-one muscle biopsies (n = 21) from healthy dogs were taken, mechanically trimmed, enzymatically dissociated with either Protease or Trypsin and cultured under identical conditions for 168 hours. To distinguish and quantify myoblasts and fibrocytes an immunocytochemical staining of the muscle cell specific intermediate filament desmin was performed. To analyse the influence of a transport on the samples eight biopsies were cultured with either Trypsin or Protease at the Using Protease a significant higher production and a morphological better proliferation of myoblasts (P = 0.0102) was achieved. The average percentage of myoblasts was 78.96% using Protease and 54.68% using Trypsin. The duration of the transport (1-3 days) did not result in any significant changes in total myoblast cell counts (P = 0.798). This reveals the possibility to send muscle biopsies from distant clinics to a specialised laboratory. In conclusion, the use of Protease is an improvement for cultivating canine myoblasts and provides better conditions for further investigations elucidating pathogenesis of rare neuromuscular diseases.