Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, the extent of presence/absence variation and the relative position of inbred-specific regions remain to be elucidated. De novo genome sequencing of the F2 maize inbred line which played a key role in European breeding programs over the past 50 years revealed thousands of novel genomic regions, making up 88Mb of DNA, that are present in the F2 but not in B73. Comparison of B73 and F2 PAV localization revealed contrasted chromosomal distributions between the two inbreds and specific evolutionary dynamics of PAVs as compared to SNPs. Detailed sequence and functional annotation of F2 PAV sequences revealed hundreds of new genes with transcriptional support, but also a large fraction of repetitive sequences. Detailed analysis of sequence breakpoint highlights the role of double strand break repair, but also transposon insertion in PAV generation. Typing of the B73 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Linkage disequilibrium (LD) analysis revealed that LD is strong within PAVs, as expected by the absence of recombination in crosses where PAV is missing in one of the parents.