Scientific papers are retracted for many reasons including fraud (data fabrication or falsification) or error (plagiarism, scientific mistake, ethical problems). Growing attention to fraud in the lay press suggests that the incidence of fraud is increasing. The reasons for retracting 742 English language research papers retracted from the PubMed database between 2000 and 2010 were evaluated. Reasons for retraction were initially dichotomised as fraud or error and then analysed to determine specific reasons for retraction. Error was more common than fraud (73.5% of papers were retracted for error (or an undisclosed reason) vs 26.6% retracted for fraud). Eight reasons for retraction were identified; the most common reason was scientific mistake in 234 papers (31.5%), but 134 papers (18.1%) were retracted for ambiguous reasons. Fabrication (including data plagiarism) was more common than text plagiarism. Total papers retracted per year have increased sharply over the decade (r=0.96; p<0.001), as have retractions specifically for fraud (r=0.89; p<0.001). Journals now reach farther back in time to retract, both for fraud (r=0.87; p<0.001) and for scientific mistakes (r=0.95; p<0.001). Journals often fail to alert the naïve reader; 31.8% of retracted papers were not noted as retracted in any way. Levels of misconduct appear to be higher than in the past. This may reflect either a real increase in the incidence of fraud or a greater effort on the part of journals to police the literature. However, research bias is rarely cited as a reason for retraction.