Laser microdissection offers the separate analysis of neuronal cells within the central nervous system in certain neurodegenerative diseases. We have established the amplification of a common deletion of mitochondrial DNA (mtDNA) on the basis of single microdissected neurons. Using brain and spinal cord tissue from patients suffering from amyotrophic lateral sclerosis (ALS) and healthy controls, we detected the 5 kB common deletion of mtDNA in motor neurons from ALS and control cases. The deletion was also present in non-motor regions from diseased patients and controls, suggesting that the presence of the mtDNA deletion is not associated with the neuronal death in specific areas of the central nervous system in ALS.