Gene expression profiling was performed in the laser capture microdissected substantia nigra pars compacta (SNc) after a single administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in common marmosets. RNA from substantia nigra pars compacta tissue underwent a double linear amplification and was then applied to a whole human genome oligo microarray. Since the number of TH-immunoreactive cells in the SNc decreased to 50% of that in the control after 14 days and since our previous study showed that down-regulation of mRNA levels precedes cell death, genes for which mRNA levels were below 50% of levels in the vehicle-treated control throughout the experimental period were defined as being vulnerable to MPTP in the present study. There were 48 genes that satisfied this condition. In order to elucidate mechanisms of dopaminergic cell death in Parkinson's disease, extensive gene expression studies at various time points after MPTP and with various MPTP doses are required.