Patients with late/very-late stent thrombosis (ST) are at high risk of recurrent-ST. The mechanisms of recurrent-ST are largely unknown. The objective is to describe the 1-year optical coherence tomography (OCT) findings of patients suffering from late/very-late ST treated with intravascular imaging guided percutaneous coronary intervention (PCI). All consecutive patients with late/very-late ST undergoing intravascular imaging guided PCI were screened to undergo coronary angiography and OCT examination at 1 year. Patients were classified according to the observation of stent malapposition as most contributing cause of the ST. Thirty-four patients were included. Stent malapposition was observed in 17 (50%) and the remaining 17 cases were classified as: neoatherosclerosis (n = 9), underexpansion (n = 3) and unknown mechanism (n = 5). Patients with malapposition had a remarkable reduction of the malapposition volume (from 6.4 to 1.3 mm³; p = 0.02) during the ST procedure, but this was not fully corrected in 13 (76.5%). At 12 months, two patients of the malapposition group presented with uneventful target vessel re-occlusion. Persistent malapposition was observed in nine patients (60.0%). Major coronary evaginations (46.7 vs. 0%; p = 0.001) and uncovered struts (6.3 vs. 1.0%; p < 0.001) were also more frequent in patients with malapposition than without malapposition. None of the patients had thin-cap fibroatheroma neoatherosclerosis. Contributing causes of late/very-late ST are diverse and have different healing patterns at 12 months. Patients with stent malapposition treated with intravascular imaging guided PCI showed poor re-healing; but patients with other causes of the ST showed optimal stent healing as assessed by OCT.