Parkinson's disease (PD) is the second most prevalent, progressive neurodegenerative disease and is characterized by the irreversible and selective loss of nigrostriatal dopaminergic (DA) neurons. Glial cell line-derived neurotrophic factor (GDNF), which is a potent protective factor for DA neurons, is considered a promising neuroprotective candidate for PD. microRNAs (miRNAs) have been shown to be involved in a number of neurodegenerative diseases. Both miRNAs and GDNF affect DA neuronal processes, but the molecular crosstalk between these molecules remains unclear. The present study aimed to evaluate whether GDNF modulates miRNA expression. We used microarray analysis and real-time polymerase chain reaction (RT-PCR) to investigate miRNAs expression in 6-hydroxydopamine (6-OHDA)-injured MN9D cells treated with GDNF for 30 min, 1 h, or 3 h. Our results showed that GDNF treatment led to differential expression of 143 miRNAs. To further identify mechanisms by which GDNF exerts its effects, we compared miRNAs and mRNAs microarray data at the 1-h time point. We found that various biological processes and pathways were regulated at the miRNA level following GDNF treatment. Collectively, these results provide evidence of the capacity of GDNF to influence miRNAs expression, suggesting a new mechanism of GDNF action.