The persistence of thrombus inside stent struts is a frequent event in patients with acute coronary syndromes (ACS) undergoing percutaneous coronary intervention (PCI), and this phenomenon might be associated with an increased risk of stent thrombosis. We sought to quantify by means of optical coherence tomography (OCT) the presence of in-stent thrombus after achievement of an optimal angiographic result in patients with ACS undergoing PCI. In addition, we evaluated the feasibility and safety of an OCT-guided strategy of in-stent thrombus removal. Eighty consecutive patients with ACS undergoing PCI were treated with two different strategies equally divided into two groups: angio-guided PCI, and OCT-guided PCI, in which additional OCT-driven in-stent balloon dilatation was adopted to reduce thrombus encroachment of the lumen. Overall in-stent thrombus area was 4.3 % with a maximal thrombus encroachment of 16.7 %. In the OCT-guided group, use of high pressure intra-stent dilatation led to a significant increase in stented area (9.6 ± 2.4 vs. 9.1 ± 2.49 mm(2), p = 0.002) and lumen area (9.2 ± 2.4 vs. 8.7 ± 2.3 mm(2), p < 0.001) and also significantly decreased in-stent thrombus area in absolute (0.35 ± 0.29 vs. 0.42 ± 0.30 mm(2), p = 0.001) and relative terms (3.58 ± 3.25 vs. 4.53 ± 3.01 %, p = 0.001). Values of TIMI flow, frame count and blush grade, as well as clinical outcomes were not detrimentally affected by such additional dilatations. The use of additional OCT-driven in-stent balloon dilatations is feasible, safe and might be effective in the treatment of in-stent thrombus for patients with ACS.