Introduction Clinical trials are the gold standard for testing the efficacy and safety of interventions. On their own they may not be enough to reach definitive conclusions, but they are the basis for systematic reviews that synthesize the results of several studies. However, once clinical trials have been published, a poor description of the study design and lack of specific key words and descriptors make it difficult to retrieve them by electronic searches, thus requiring hand searching. Objectives To compare the retrieving capacity between hand search and the multiple strategies of electronic searches for identifying clinical trials in Cuban medical journals, and to determine the terminology used for describing these studies. Methods We combined electronic searches in the Scientific Electronic Library Online of Cuba (SciELO Cuba) and Cuban database Cumed with hand search using the Cochrane guide to locate trials in three Cuban journals in the period 2000-2012. We identified the significant terms included in the title, summary, keywords and methods of each article according to Cochrane, CONSORT, and the health sciences thesaurus. Results We identified 50 trials by hand search; four of them were retrieved by electronic search through SciELO Cuba (8%) while none was found through Cumed. The less descriptive sections were the title and the keywords. More keywords than authorized descriptors were used; the only specific concepts used in over half of the retrieved trials were "controlled" (60%), and "study groups" (52%); "randomized" was used in 50% of the retrieved documents. While more specific, the terms "clinical trial", "phase", and "clinical trial registration" were not used. Conclusions Compared to hand searching, electronic searches are insufficient to identify clinical trials. Therefore, the combination of the two methods is necessary to reach higher retrieval rates. The terminology used to describe clinical trials in the selected journals was deficient due to underutilization of the health sciences thesaurus.