RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms. Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which produces variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. Here we leverage publicly available data to perform a Genome-Wide Association Study of the utilisation of more than 16000 individual splice-sites across the Arabidopsis transcriptome; identifying in excess of 6000 associations. We report numerous patterns identified from this new dataset, including strong evidence for the cis-, rather than trans-, genetic variation driving splice site choice.