MOTIVATION: Changes in genome organisation contribute to genetic disease when they disrupt gene function or regulation. Structural rearrangements may interrupt coding sequence or alter expression through promoter loss or gain, chromatin changes, copy-number variation, or disruption of short-range regulatory elements. Although short-read sequencing excels at detecting small variants, it performs poorly at resolving breakpoints of large rearrangements, especially in repetitive or low-complexity regions. Long-read sequencing overcomes these limitations, but analytical tools have not kept pace, making accurate identification and annotation of large structural variants challenging. RESULTS: We developed AgileStructure, a desktop application for locating and annotating large‑scale genomic rearrangements using aligned long‑read data. The software enables user‑guided exploration of breakpoint‑spanning reads, supporting accurate interpretation of complex events and filling a key gap in current structural variant analysis workflows. AVAILABILITY AND IMPLEMENTATION: Source code, binaries, user guide, and example aligned read data, are available on GitHub: https://github.com/msjimc/AgileStructure. An archived version is also available on Zenodo at https://doi.org/10.5281/zenodo.18610110.