Background: Mutations of the leucine rich repeat kinase 2 (LRRK2) gene are the most common genetic cause of Parkinson’s disease (PD) and are associated with pleiomorphic neuropathology. We hypothesise that LRRK2 mediates its pathogenic effect via alternative splicing of neurodegeneration genes. Methods: Western blot analysis of subcellular protein fractions. Exon-array analysis of RNA from cultured neuroblastoma cells transfected with LRRK2 expression vectors. Reverse-transcription PCR (RT-PCR) of RNA from cultured cells and post-mortem tissue. Results: Over-expression of LRRK2 G2019S mutant resulted in a significant 2.6 fold (p = 0.020) decrease in nuclear TDP-43 levels. Exon-array analyses revealed that wildtype LRRK2 had a significant effect on expression of genes with nuclear (p < 10-22) and cell cycle functions (p < 10-15). We replicated changes in gene expression in 30% of selected genes by quantitative RT-PCR. Over-expression of LRRK2 resulted in altered splicing of two genes associated with PD, with an increased inclusion of exon 10 of MAPT (1.7 fold; p =0.001) and exon 5 of the SNCA gene (1.6 fold; p =0.005). Moreover, over-expression of LRRK2 (G2019S), TARDBP (M337V) and FUS (R521H) mutants was associated with decreased inclusion out of the DST 1e precursor exons in SK-N-MC cells. Altered splicing of SNCA (1.9 fold; p < 0.001) and DST genes (log2 2.3 fold; p = 0.005) was observed in a cohort of PD compared with neurologically normal brains. Conclusions: Our study highlights the importance of aberrant RNA metabolism as a common pathogenic pathway for idiopathic PD, mediated in part by LRRK2 dysfunction.