Stem lodging causes significant losses in crops of cereals and oilseeds. The aim of the present study was to identify the anatomical causes that generate differences in response to stem lodging in sunflower. Two sunflower hybrids (Stay-Green, resistant to stem lodging; Zenit, susceptible to stem lodging) were grown at three crop population densities and artificially lodged at two advanced ontogeny stages (R7 and R8), which were preceded by ethephon application near the flower button stage (R1). Measurements included stem failure moment of force (Bs), thickness of primary and secondary structures in the stem lodging zone (t), diameter of the stem lodging zone (di), sclerenchyma packages area (sp), secondary xylem tissue area (xt) and yield. Stay-Green had significantly higher values for Bs, t, di, sp and xt. At higher crop densities and more advanced ontogeny stages these parameters were reduced, favouring stem lodging, although the effects were ameliorated by ethephon application through anatomical modifications. Zenit exhibited the greatest responses to ethephon application. The present study is the first field study identifying anatomical changes causing stem lodging and intraspecific variability in sunflowers. The information provided can be used by geneticists in selection programs for stem lodging tolerance in the context of increasing crop population densities to improve sunflower yield.