Next generation sequencing provides a unique opportunity to understand gene expression. Solexa RNAseq was used to look into gene expression differences that occur in the wheat variety Thatcher when infected with different races of leaf rust. Six races were selected from the North American 5 linage, single pustule purified, and inoculated individually onto 2-3 leaf stage seedlings of the hard red spring wheat, Thatcher. At six days post inoculation, leaves were sampled and total RNA was isolated and sent to Cofactor Genomics. A single lane of paired end read Illumina GAIIx sequencing was performed for each race. Each race averaged 27.4 million reads and 3.295 million base pairs. Reads were aligned to the Puccinia triticina genome and a wheat EST data set. Pairwise comparisons were made. Data will be reported.