Understanding the publication output of a country's biomedical research can provide information for strengthening its policies, economy, and educational systems. Yet, this is the first bibliometric study to date to analyze and provide an in-depth discussion of the biomedical research productivity from Libyan academic institutions. The biomedical research productivity of higher education institutes and affiliated hospitals from Libya, with a focus on the higher education sector, was analyzed and discussed for the period of 2003-13 using the PubMed database. A questionnaire online survey was also developed to obtain opinions of Libyan scientists on productivity status and quality of research output. A total of 345 peer-reviewed articles were included in the analysis and were authored by researchers in the cities of Benghazi (32%), Tripoli (29%), Al-Zawiya (9%), Al-Bayda (8%), Sabha (3%), Misrata (3%), and Al-Khoms (1%). The papers included co-authors and/or corresponding authors from over 40 other countries were published in 179 journals covering a broad range of biomedical topics. Questionnaire (44% response rate) indicated research is largely self-funded. Information along with accurate, comprehensive, and transparent metrics can be applied to aid governmental and nongovernmental institutions to develop stable infrastructures for academic communities to achieve effective research performance and innovation.