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Background Influenza serologic diagnosis is mainly based on hemagglutination inhibition and microneutralization methods, both methods require handling living viruses under an enhanced biosafety level. Aim The current study was performed for developing an ELISA using synthetic peptides to detect influenza A H1N1 virus 2009 specific antibodies in serum and saliva. Methods Alignments were made with H1N1 hemagglutinin and neuraminidase (HA and NA, respectively) sequences; only conserved sites were used for antigenicity prediction. Two synthetic peptides were assayed; one of neuraminidase (NA15) and one of hemagglutinin (HA-15) and used in ELISA for detecting IgG and IgA antibodies. A cross-sectional study was performed in three municipalities of Mexico City, using negative samples collected before the 2009 influenza outbreak, samples of people who became ill during the outbreak, and samples of the participants in the epidemiological study with or without symptoms. Results The determination of serum IgG antibodies with both peptides allowed differentiating between the post outbreak groups with respect to all others. No differences were found in IgA determination in saliva against both peptides. The frequency of positive participants for NA-15 was 9.5 and 8.8% for HA-15 in serum IgG; whereas the frequency of positive participants for NA-15 was 11%, and for HA-15 was 8.6% for saliva IgA. Conclusions Synthetic peptides of the neuraminidase and hemagglutinin proteins can be used in ELISA for the determination of IgG and IgA antibodies against the influenza A H1N1 virus 2009.