Alternative splicing (AS) is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Different types of AS have been observed; these include exon skipping, alternative donor or acceptor site and intron retention. In humans, exon skipping is the most common type while intron retention is rare. In contrast, in Arabidopsis, intron retention is the most prevalent AS type (approximately 40%). Here we show that direct transcript expression analysis using high-density oligonucleotide-based whole-genome microarrays (WGAs) is particularly amenable for assessing global intron retention in Arabidopsis. By applying a novel algorithm retained introns are detected in 8% of the transcripts examined. A sampling of 14 transcripts showed that 86% can be confirmed by RT-PCR. This rate of detection predicts an overall total AS rate of 20% for Arabidopsis compared with 10-22% based on EST/cDNA-based analysis. These findings will facilitate monitoring constitutive and dynamic whole-genome splicing on the next generation WGA slides.