Aims: Subacute, late, and very late stent thrombosis (ST) may occur after stent implantation, but they are characterised by different underlying pathophysiological mechanisms. We sought to appraise differences between subacute and late/very late ST at the thrombus site by optical coherence tomography (OCT). The Mechanism Of Stent Thrombosis (MOST) study was a prospective multicentre non-randomised registry which enrolled six subacute ST and six controls (subacute ST study), and 17 late/very late ST and 17 controls (late/very late ST study). Methods and results: Patients with subacute ST had a minimum stent area at the thrombus site of 2.1 mm(2) (1st-3rd quartile 1.3-4.5) vs. 2.9 mm(2) (2.4-5.0) in the matched control (p=0.05). Uncovered struts were 26.2% (16.5-35.9) vs. 13.9% (8.9-18.9), p=0.001. Malapposed struts were 18.8% (13.1-24.5) vs. 15.2% (12.8-17.6), p=0.001. In patients with late/very late ST, uncovered struts were 23.6% (13.9-33.3) vs. 5.2% (0.5-10.2), p=0.001. Malapposed struts were 12.1% (6.4-17.8) vs. 2.8% (0.4-5.2), p=0.001, and maximum malapposition distance was 0.45 mm (0.32-0.62) vs. 0.12 mm (0-0.25), p=0.01. Notably, all patients with ST had previously discontinued dual antiplatelet therapy (n=14) or showed high residual platelet reactivity on clopidogrel therapy. Conclusions: Subacute ST had a significant stent underexpansion while late/very late ST had a greater stent strut malapposition distance at the thrombus site. These findings explain how procedure-related complications and vessel remodelling have a specific impact on the segment characterised by thrombus. High platelet reactivity also seems a necessary cofactor for both subacute and late/very late ST.