The purpose of this study was to evaluated the clinical characteristics of calcified nodule-like in-stent restenosis (ISR) lesions using optical coherence tomography (OCT) in vivo. A total of 124 ISR lesions that were treated with a repeat coronary intervention under OCT guidance were included in this analysis. ISR neointimal morphology was classified as “calcified nodule-like ISR”, that appeared as a high-backscattering protruding mass with an irregular surface covered by signal-rich bands, or “non-calcified nodule-like ISR”. The maximum arc and thickness of calcium behind the stent struts was also measured. Of the 124 ISR lesions, calcified nodule-like ISR was observed in 11 lesions (9%). OCT analysis data showed that the maximum arc of calcium and the maximum calcium thickness behind the stent were significantly larger in the calcified nodule-like ISR lesions than in the non-calcified nodule-like ISR lesions (269 ± 51 vs. 179 ± 92°, p < 0.01 and 989 ± 174 vs. 684 ± 241 μm, p < 0.01, respectively). The enlargement of the stent area was significantly larger in the calcified nodule-like ISR lesions than in the non-calcified nodule-like ISR lesions (1.6 ± 2.3 vs. 0.7 ± 1.3 mm 2 , p = 0.02). As a result, the enlargement of the lumen area tended to be larger in the calcified group (2.8 ± 1.7 vs. 2.4 ± 1.3 mm 2 , p = 0.3). Calcified nodule-like neointima within the stent could develop in approximately 10% of all ISR lesions, especially within stents deployed in severely calcified lesions.