Collagen Q (ColQ) is the non-catalytic subunit of acetylcholinesterase asymmetric molecu­lar forms. We examined ColQ expression in the extrajunctional and junctional regions of innervated and non-innervated regenerating fast sternomastoid (STM) and slow soleus (SOL) muscles. In two groups of rats, the SOL and STM muscles were denervated before injury, whereas in three groups the muscle nerve was left intact. The muscles were injured by cut­ting all their blood vessels and by injecting a myotoxic anesthetic bupivacaine. The regenerating muscles were isolated for 10 or 60 days after injury. The ColQ mRNA levels were determined by quantitative reverse transcription polymerase chain reaction. The extrajunctional ColQ mRNA levels in the non-innervated regenerating STM and SOL muscles were not significantly different. A short-term innervation increased extrajunctional ColQ mRNA levels of both regen­erating muscles in comparison to non-innervated regenerates, but the levels were higher in the SOL muscle than in STM muscle (p < 0.01). A long-term innervation of STM muscle regen­erates decreased the extrajunctional ColQ mRNA levels (p < 0.01). ColQ mRNA levels in the extrajunctional and former junctional regions of non-innervated regenerating STM muscles were not significantly different, however, they became significantly higher in the junction­al regions than in the extrajunctional regions after 60 days of innervation (p < 0.01). Intrinsic difference between the myogenic precursor cells of fast and slow muscles may be the rea­son for different response of immature regenerating muscles to innervation. The signaling mechanism, which regulates ColQ expression in the fast muscle junctional regions, originates from the motor nerve terminals also during maturation of regenerating muscle fibers.