Progress in molecular breeding of potato has been limited due to its complex genetics and high heterozygosity. To explore natural variation of quantitative potato late blight resistance and to discover contributing genes, we took advantage of recent advances in high-throughput sequencing technologies using SuperSAGE and RNASeq. SuperSAGE yielded the transcriptome of 4 P. infestans challenged genotype pools, consisting of 39 individuals out of 500 late blight genotypes after marker assisted selection, and provided approximately 3 Mio tags per analyzed library. Pair wise comparisons between and within genotypic groups over the infection time course resulted in 1000 to 4000 differentially regulated transcripts (p<10-6). Novel regulated candidate transcripts without any known functional description in the context of late blight resistance were verified by qRT-PCR. RNASeq analysis of 4 normalized cDNA libraries, which were constructed by picking 8 out of the 39 pre-selected individuals, resulted in 221 Mio reads with an average library size of 55 Mio reads. All together, 325.000 single nucleotide polymorphisms (SNPs) were identified from which 3366 were significantly (p<0.05) different between quantitative less and quantitative more resistant genotypes. Furthermore, 1407 genes contained at least 1 significant SNP. Polymorphic candidate transcripts were verified by PCR and will be used for future association analysis. Both transcriptome approaches combined expressional profiling and SNP calling of novel candidate transcripts differentially present in genotypes with contrasting quantitative resistance to late blight. This facilitates molecular breeding towards durable and broad spectrum resistance, and will provide DNA markers for potato ‘precision breeding’.