Experimental models of Parkinson's disease (PD) created by aberrant expression of the alpha-synuclein (SNCA) coding region have been reported. However, noncoding regions function in normal physiology and recent in vitro studies have shown that microRNAs-7 and -153 regulate SNCA expression by binding the 3'UTR. Here, effects of different hSNCA forms were examined in vivo. Adult, male rats were injected into one substantia nigra (SN) with AAV-wtSNCA, AAV-S129A hSNCA, or AAV-S129D hSNCA either with or without a portion of the native 3'UTR. DA neurons in SN that maintained striatal (ST) projections at the end of treatment were retrogradely labeled by bilateral ST fluorogold (FG) injections and FG-positive DA neurons in SN were counted. At 5 weeks, hSNCA coding vectors reduced numbers of FG-positive neurons in injected SN compared with uninjected SN (wtSNCA, p = 0.05; S129A/D hSNCA, p = 0.01). At 7 and 9 weeks, wtSNCA- and S129D hSNCA-treated rats exhibited recovery, but S129A hSNCA-injected rats did not (p = 0.01). In contrast, numbers of FG-positive neurons were unaffected by hSNCA expression when the 3'UTR was included. When FG-positive neurons were expressed as the ratio of numbers in injected to uninjected sides, the S129A hSNCA coding vector resulted in the highest decrease at 9 weeks versus wtSNCA (p = 0.05) or S129D hSNCA (p = 0.01). Inclusion of the 3'UTR resulted in no significant differences in FG-positive neuron ratios. These data suggest that inclusion of the 3'UTR protects against S129A hSNCA-induced loss of nigrostriatal-projecting DA neurons in vivo and that mis-regulation of hSNCA expression and function at noncoding regions contribute to PD pathogenesis. (c) 2011 Wiley Periodicals, Inc. Develop Neurobiol 72: 906-917, 2012.