The purpose of this research was to identify and characterize resistance gene analogs (RGAs) in tomato by PCR amplification of genomic DNA using primers designed based on the conserved amino-acid domains of several known plant disease resistance genes (R genes). Amplified DNAs from a Lycopersicon esculentum × L. hirsutum backcross (BC1) population were separated by denaturing polyacrylamide gel electrophoresis (PAGE). Polymorphic bands were scored as DNA markers and were positioned on a tomato genetic map. Several markers were located in the vicinity of previously identified tomato R genes and quantitative resistance loci (QRLs). Polymorphic and monomorphic bands were isolated, cloned and sequenced. Nucleotide sequences of several of the clones revealed homology to known R genes, RGAs, defense-related genes, or other plant genes. A majority of the clones, however, did not exhibit sequence homology with known R genes in the database, suggesting that PCR amplification using resistance gene primers results in products which are not related to disease resistance. The utility of PAGE-polymorphic and PAGE-monomorphic bands as genetic markers and potential candidates for positional gene cloning is discussed.