Background Insertions/deletions (indels), and more specifically presence/absence variations (PAVs) are pervasive in maize and have strong functional and phenotypic effect by removing or modifying drastically genes. Genotyping of such variants on large panels remains poorly addressed, while necessary for approaches such as association mapping or genomic selection. Results We have developed a new high throughput and cost-effective tool to genotype indel. We first identified 141,000 indels by aligning reads from the B73 line against the genome of three temperate maize inbred lines (F2, PH207, and C103) and reciprocally. Next, we designed an Affymetrix® Axiom® array to target these indels with a combination of probes selected at breakpoint sites (13%) and/or within the indel sequence either at polymorphic (25%) or non-polymorphic sites (63%) sites. The final array design is constituted of 662,772 probes and targets 105,927 indels including PAVs, ranging from 35bp to 129kbp. After Affymetrix® quality control, we successfully genotyped 89,393 indels (84%) on 445 maize DNA samples with 479,027 probes (72%). A principal coordinate analysis on dissimilarity estimated from a subset of 57,824 indels on 362 inbred lines is consistent with the structure obtained using 50K SNP arrays. Conclusions We efficiently genotyped thousands of small to large indels on a large number of individuals using a new Affymetrix® Axiom® array. This powerful tool opens the way to studying the contribution of indels to trait variation and heterosis in maize. The approach is easily extendable to other species and should contribute to decipher the biological impact of indels at a larger scale.