Background: Acute myocardial infarction (MI) is a leading cause for morbidity and mortality in Sweden. We aimed to compare patients with an acute MI included in the Register of information and knowledge about Swedish heart intensive care admissions (RIKS-HIA, now included in the register Swedeheart) and in the Swedish statistics of acute myocardial infarctions (S-AMI). Methods: Population based register study including RIKS-HIA, S-AMI, the National patient register and the Cause of death register. Odds ratios were determined by logistic regression analysis. Results: From 2001 to 2007, 114,311 cases in RIKS-HIA and 198,693 cases in S-AMI were included with a discharge diagnosis of an acute MI. Linkage was possible for 110,958 cases. These cases were younger, more often males, had fewer concomitant diseases and were more often treated with invasive coronary artery procedures than patients included in S-AMI only. There were substantial regional differences in proportions of patients reported to RIKS-HIA. Conclusions: Approximately half of all patients with an acute MI were included in RIKS-HIA. They represented a relatively more healthy population than patients included in S-AMI only. S-AMI covered almost all patients with an acute MI but had limited information about the patients. Used in combination, these two registers can give better prerequisites for improved quality of care of all patients with acute coronary syndromes.