Single-nucleotide polymorphisms (SNPs) are the most frequent variations in the genome of any organism. SNP discovery approaches such as resequencing or data mining enable the identification of insertion deletion (indel) polymorphisms. These indels can be treated as biallelic markers and can be utilized for genetic mapping and diagnostics. In this study 655 indels have been identified by resequencing 502 maize (Zea mays) loci across 8 maize inbreds (selected for their high allelic variation). Of these 502 loci, 433 were polymorphic, with indels identified in 215 loci. Of the 655 indels identified, single-nucleotide indels accounted for more than half (54.8%) followed by two- and three-nucleotide indels. A high frequency of 6-base (3.4%) and 8-base (2.3%) indels were also observed. When analysis is restricted to the B73 and Mol7 genotypes, 53% of the loci analyzed contained indels, with 42% having an amplicon size difference. Three novel miniature inverted-repeat transposable element (MITE)-like sequences were identified as insertions near genes. The utility of indels as genetic markers was demonstrated by using indel polymorphisms to map 22 loci in a B73 x Mo17 recombinant inbred population. This paper clearly demonstrates that the resequencing of 3' EST sequence and the discovery and mapping of indel markers will position corresponding expressed genes on the genetic map.