Few studies have directly compared vascular responses to second-generation drug-eluting stents (DESs). We performed optical coherence tomography examinations in 56 consecutive patients with implanted single stent [19 cobalt-chromium everolimus-eluting stents (CoCr-EES), 22 platinum-chromium EES (PtCr-EES), and 15 resolute zotarolimus-eluting stents (R-ZES)] for de novo lesions, and who did not have restenosis at their 9-month follow-up. Neointimal thickness (NIT), stent apposition, and neointimal coverage were assessed in every strut. A neointimal unevenness score [(NUS), maximum NIT/average NIT in the same cross-section] was determined for every 1-mm cross-section (CS). A total of 8350 struts and 1159 CSs were analyzed. The CoCr- and PtCr-EES had significantly fewer malapposed struts compared to the R-ZES (CoCr-EES: 0.19 % vs. PtCr-EES: 0.19 % vs. R-ZES: 0.61 %, p = 0.007). Furthermore, the PtCr-EES had a lower frequency of uncovered struts compared to the others (CoCr-EES: 2.0 % vs. PtCr-EES: 1.4 % vs. R-ZES: 2.3 %, p = 0.047). The NUS correlated with the frequency of uncovered struts (p < 0.001, r = 0.54). The EESs demonstrated more homogenous neointimal growth, as shown in the NUS, compared to the R-ZES [CoCr-EES: 1.66 (1.38–1.97) vs. PtCr-EES: 1.67 (1.41–2.00) vs. R-ZES: 1.94 (1.56–2.28), p < 0.001]. Our results demonstrate that unevenness neointimal growth may relate with strut coverage after second-generation DES implantation. The PtCr-EES had a high frequency of strut coverage with a homogeneous neointima, suggesting fewer risks for stent thrombosis.