With this study, we were able to identify the main reasons for issuing a modified audit opinion in relation to companies listed on BM&FBovespa, the Brazilian stock market. To this end, the financial statements of all the companies listed in 2013, 2014 and 2015 were analysed through a descriptive study with a qualitative approach and documentary research. The findings of the research highlight that the main factors that lead to the issue of modified audit reports are problems in the application of asset recoverability tests, inconsistencies in the balances and values of tax and labour (social) obligations, lack of external confirmation, problems with understating liabilities, problems with the recognition and reclassification of accounting accounts, the existence of judicial recovery processes, accumulated losses and overdrawn liabilities. It should be emphasised that these factors cause the auditors to have doubts about the company's ability to continue as a going concern, thus issuing modified reports in the form of a report with reservations, an adverse report or a report abstaining from an opinion.