Application of extracorporeal shockwaves to the musculoskeletal system can induce long-term analgesia in the treatment of chronic painful diseases such as calcifying tendonitis of the shoulder, tennis elbow and chronic plantar fasciitis. However, the molecular and cellular mechanisms underlying this phenomenon are largely unknown. Recently it was shown that application of extracorporeal shockwaves to the distal femur of rabbits can lead to reduced concentration of substance P in the shockwaves' focal zone. In the present study we investigated the impact of extracorporeal shockwaves on the production of substance P within dorsal root ganglia in vivo. High-energy shockwaves were applied to the ventral side of the right distal femur of rabbits. After six weeks, the dorsal root ganglia L5 to L7 were investigated with high-precision design-based stereology. The application of extracorporeal shockwaves caused a statistically significant decrease in the mean number of neurons immunoreactive for substance P within the dorsal root ganglion L5 of the treated side compared with the untreated side, without affecting the total number of neurons within this dorsal root ganglion. No effect was observed in the dorsal root ganglia L6 and L7, respectively. These data might further contribute to our understanding of the molecular and cellular mechanisms in the induction of long-term analgesia by extracorporeal shockwave application to the musculoskeletal system.