objective: the objective of this study was to determine the application of gender perspective in public health papers in four journals published by the mexican national health institutes. material and methods: a total of 999 papers published in the four journals between 2000 and 2003 was reviewed. two levels of analysis were considered: a) data presented by sex, providing description of differences between women and men, and b) the analysis of these differences from gender perspective. results: one quarter (25.4%) of the articles described results by sex. the largest percentage was published in salud pública de méxico (48.8%) and the smallest in revista de investigación clínica (16.1%). gender perspective was used in only 4.2% of papers; of these, drug addictions, health behaviour and violence were the topics that occurred most frequently. conclusions: this is the first study to assess the application of gender perspective in mexican health articles. similarly to other countries, a very small percentage of authors analyzed sex differences, and a smaller proportion applied gender perspective. results demonstrate the importance of promoting interdisciplinary research that may promote the elucidation of health inequalities between men and women.