The present study aimed to investigate the relationship between traditional citation indexes representing hot papers in the field of “Clinical Medicine” and their bookmarking and readership in “Mendeley software”. The citation counts of hot papers were extracted from Essential Science Indicators (ESI) and Web of Science (WoS). As an applied research adopting a descriptive-exploratory method, the present study used the Essential Science Indicators to retrieve hot articles published between 2014 and 2016, indexed in the category “Medical Sciences”. Each record was then searched in Mendeley to obtain the number of readership of the paper and the academic status of the users. The results showed a significant positive correlation between Mendeley readership and citation indexes in both ESI and WoS. Moreover, the most frequently-cited articles in both databases attracted more readers in Mendeley than lowly-cited publications and both hypotheses were confirmed. Moreover, the findings revealed that Mendeley users had assigned a total number of 3847 tags to the hot papers, with the tags ranging in frequency from zero to 38 for individual articles. Compared with author keywords and Plus, about 10 percent of users’ tags were either meaningless or repetitive. The value of present study shows that “Mendeley Sofware” with the possibility of tagging articles, can be used to create a searchable folksonomy of information and as a source of data in information retrieval studies, help professionals to manage their literatures and make their research life easier.