Fragmented QRS (fQRS) may occur due to non-homogeneous activation of ischemic ventricles. We want to investigate the prognostic significance of a fQRS complex in a patient who had undergone primary percutaneous coronary intervention (PCI). Eighty-five patients with no history of coronary artery disease who underwent primary PCI were included in the study. Of these patients, 34 who were found to have a fQRS at the 48th hour after primary PCI were defined as group 1, and 51 who were found not to have a fQRS were defined as group 2. Both groups were monitored for adverse cardiac events. At 6.6 ± 2.3 months of follow-up, major adverse cardiac events (MACE) was found significantly higher in the fQRS group [group 1:10 (29.4%) vs. group 2:3 (5.9%); p:0.003]. In multivariate Cox regression analysis; the duration of chest pain (HR:1.02, CI:1.004-1.05; p = 0.03) and fQRS at 48th hour (HR 7.16, CI 3.17–20.11; p = 0.006) were predictors of MACE. In the group 2, event-free survival rate was found significantly higher; however, Q wave and QRS distortion were found to be insignificant with regard to demonstrating event-free survival. Compared to both Q wave and QRS distortion, fQRS showed high sensitivity and specificity in demonstrating MACE (sensitivity 0.77; specificity 0.67; AUC 0.71 (0.57–0.86); p 0.01). fQRS had 73% sensitivity and 49% specificity and Q wave had 58% sensitivity and 85% specificity for demonstrating the presence of scar on myocardial perfusion scintigraphy with ROC curve analysis. The presence of a fQRS at the 48th hour is a significant predictor of MACE in patients with ST elevation myocardial infarction who have undergone primary PCI. (ClinicalTrials.gov number: NCT01136837).