During the spring of 2009, H1N1 influenza became the first pandemic of the 21st century. There are no bibliometric studies in Mexico that have analyzed this topic in relation to the generation of Mexican knowledge. The aim of this article is to determine the volume and impact of Mexican scientific output published in journals indexed in Science Citation Index (SCI) on influenza from January 1, 2000, to October 1, 2012. All the documents within SCI whose topic was influenza were included; in order to do this, we used the describers influenza or swine flu H1N1. The analysis included authorship, international collaboration, journals, document type, citations and address of correspondence. In 2000-2012, 241 articles related to influenza were published. The years with the highest number of articles were 2009 (n = 53) and 2010 (n = 62). The journals with the highest quantity of papers were Salud Pública de México (n = 16), PLOS ONE (n = 13), Archives of Medical Research (n = 13) and Vaccine (n = 10). The most investigated area was infectious diseases (18.9 %), followed by internal medicine (14 %) and immunology (14 %), occupational health (13 %) and experimental medicine (12.3 %). The scientific output on influenza supposes near 1 % of the total of the medical-scientific production with a decline posterior to the outbreak of 2009 pandemic influenza.