Inbreeding depression has severe consequences to the genomic make-up of an organism, such as a reduction in genome size and purging of deleterious mutations. The purpose of this study was to track these genomic changes during the transition from outcrossing to self-fertilization. Since transposable elements (TEs) are deleterious, we expected that they would be purged and possibly cause the decline in genome size. To investigate this, we first used flow cytometry on the first six generations in 11 selfing landraces of maize (Zea mays). We found that three of the maize lines had a significant decrease in genome size, up to 20%, yet there was no significant change in the other lines. Next, to establish the cause for this reduction, we performed whole-genome sequencing on S1 and S6 generations, including all three with a genome size reduction. The sequenced reads were mapped to annotated genes, exemplar transposable elements, knob repeats and rDNA. We found in all the lines that there was indeed a loss in TE content. In addition, landraces that did not show a decrease in genome size contained more knob repeats and these knob repeats increased over generations. These results show there are changes in genomic content including TEs as a repercussion of selfing.