Reporting research limitations in academic literature is very important for understanding and utilizing research findings. This study aims to assess the extent to which and how research limitations acknowledged in Persian theses and dissertations (TDs). 664 Persian TDs published from 2009 to 2018 selected randomly through cluster sampling technique from IranDoc’s TDs database and the last chapter of 578 TDs analyzed. Through content analysis method, reported limitations analyzed and coded. Around 17% of TDs (99/578) addressed at least one limitation in their reports, while 64% of them had a specific heading for this section. The trend of reporting limitations has increased during current decades and students in humanities areas have paid more attentions to this section. Overall, 22 key limitations have been repeated 268 times in the TDs and “sampling bias” is more frequent with 29 repeats among them. Addressing research limitations in TDs is very incomplete. Transparent addressing of research limitations may help readers and stakeholders understand and apply research findings more effectively. The role of educators and academic institutes to inform newcomer researchers about the importance and structure of research limitations section in their reports is vital. This is the first study to examine research limitations in Persian academic literature and can inspire more research on this subject. The stakeholders of research, such as faculties, students, universities, research centers, readers/beneficiaries, and sponsors will be informed about key research limitations in TDs.