Background Evidence indicates that early reperfusion therapy in patients with ST-elevation myocardial infarction (STEMI) reduces complications. This study was undertaken to compare the in-hospital delay to primary percutaneous coronary intervention (PPCI) for patients with STEMI between specialized hospitals and non-specialized hospitals in Beijing, China. Methods Two specialized hospitals and fifteen non-specialized hospitals capable of performing PPCI were selected to participate in this study. A total of 308 patients, within 12 hours of the onset of symptoms and undergoing PPCI between November 1, 2005 and December 31, 2006 were enrolled. Data were collected by structured interview and review of medical records.Results The median in-hospital delay was 98 (interquartile range 105 to 180) minutes, and 16.9% of the patients were treated within 90 minutes. Total in-hospital delay and ECG-to-treatment decision-making time were longer in the non-specialized hospitals than in the cardiac specialized hospitals (147 minutes vs. 120 minutes, P<0.001; 55 minutes vs. 45 minutes, P=0.035). After controlling the confounding factors, the non-specialized hospitals were independently associated with an increased risk of being in the upper median of in-hospital delays.Conclusions There were substantial in-hospital delays between arrival at the hospital and the administration of PPCI for patients with STEMI in Beijing. Patients admitted to the cardiac specialized hospitals had a shorter in-hospital delay than those to the non-specialized hospitals because of a shorter time of ECG-to-treatment decision-making.