NBS proWling is a method for the identiWcation of resistance gene analog (RGA) derived fragments. Here we report the use of NBS proWling for the genome wide mapping of RGA loci in potato. NBS proWling analyses on a minimal set of F1 genotypes of the diploid mapping population previously used to generate the ultra dense (UHD) genetic map of potato, allowed us to eYciently map polymorphic RGA fragments relative to 10,000 existing AFLP markers. In total, 34 RGA loci were mapped, of which only 13 contained RGA sequences homologous to RGAs genetically positioned at approximately similar positions in potato or tomato. The remaining RGA loci mapped either at approximate chromosomal regions previously shown to contain RGAs in potato or tomato without sharing homology to these RGAs, or mapped at positions not yet identiWed as RGA-containing regions. In addition to markers representing RGAs with unknown functions, segregating markers were detected that were closely linked to four functional R genes that segregate in the UHD mapping population. To explore the potential of NBS proWling in RGA transcription analyses, RNA isolated from diVerent tissues was used as template for NBS proWling. Of all the fragments ampliWed approximately 15% showed putative intensity or absent/present diVerences between diVerent tissues suggesting putative tissue speciWc RGA or R gene transcription. Putative absent/present diVerences between individuals were also found. In addition to being a powerful tool for generating candidate gene markers linked to R gene loci, NBS proWling, when applied to cDNA, can be instrumental in identifying those members of an R gene cluster that are transcribed, and thus putatively functional.