Analysing scientific production in the area of infectious diseases in Colombia, 2000-2009.A literature search was made in category A journals in Colciencias' Publindex. The journals were: Biomédica, Revista de Salud Pública (Universidad Nacional), Colombia Médica, Ciencias Pecuarias, Latreia, MVZ Córdoba, Revista de Medicina (Universidad Nacional) and Infectio.2,963 publications were found; 2,744 (92.6 %) were national publications and 219 (7.4 %) were foreign submissions, of which 863 (29.1 %) were on infectious diseases, 817 (94.7 %) having been submitted nationally and 46 (5.3 %) submitted by foreigners. National publications on infectious diseases were distributed as follows: 268 on parasitology (32.8 %), bacteriology and antimicrobial resistance accounted for 267 (32.7 %), virology 210 (25.7 %), mycology 46 (5.6 %) and other items related to infectious diseases accounted for 26 (3.2 %). The regional distribution of publications was: Cundinamarca 239 (29.3 %), Antioquia 211 (25.8 %), Valle del Cauca 60 (7.3 %), Caribbean coast 52 (6.4 %), the Santanders 38 (4.6 %), the coffee-growing area 31 (3.8 %) and southern Colombia 13 (1.6 %).This is the first study which has analysed publications on infectious diseases in Colombia. There was regional imbalance concerning bibliometric indicators in Colombia; public universities accounted for 90 % of research being carried out in the area of infectious diseases in Colombia.