To assess the prevalence of plagiarism in manuscripts submitted for publication in the Croatian Medical Journal (CMJ). All manuscripts submitted in 2009-2010 were analyzed using plagiarism detection software: eTBLAST, CrossCheck, and WCopyfind. Plagiarism was suspected in manuscripts with more than 10% of the text derived from other sources. These manuscripts were checked against the Déjà vu database and manually verified by investigators. Of 754 submitted manuscripts, 105 (14%) were identified by the software as suspicious of plagiarism. Manual verification confirmed that 85 (11%) manuscripts were plagiarized: 63 (8%) were true plagiarism and 22 (3%) were self-plagiarism. Plagiarized manuscripts were mostly submitted from China (21%), Croatia (14%), and Turkey (19%). There was no significant difference in the text similarity rate between plagiarized and self-plagiarized manuscripts (25% [95% CI 22-27%] vs. 28% [95% CI 20-33%]; U = 645.50; P = 0.634). Differences in text similarity rate were found between various sections of self-plagiarized manuscripts (H = 12.65, P = 0.013). The plagiarism rate in the Materials and Methods (61% (95% CI 41-68%) was higher than in the Results (23% [95% CI 17-36%], U = 33.50; P = 0.009) or Discussion (25.5 [95% CI 15-35%]; U = 57.50; P < 0.001) sections. Three authors were identified in the Déjà vu database. Plagiarism detection software combined with manual verification may be used to detect plagiarized manuscripts and prevent their publication. The prevalence of plagiarized manuscripts submitted to the CMJ, a journal dedicated to promoting research integrity, was 11% in the 2-year period 2009-2010.