<i>Background:</i> Evidence of the influence of pathogen exposure on the development of atopy and atopic disease is not unequivocal. We investigated the association between markers of infections and occurrence of atopy among adults in eastern Finland and western Russia, two adjacent areas with profound differences in living conditions and lifestyles. <i>Methods:</i> Randomly selected adults aged 25–54 years from Finland (n = 790) and from Russia (n = 387) participated in the study. Skin prick tests were performed to 11 common airborne allergens, and at least one positive prick reaction was considered to indicate atopy. Antibodies to different pathogens including hepatitis A virus (HAV), <i>Helicobacter pylori, Toxoplasma gondii</i>, herpes simplex virus (HSV), <i>Chlamydia pneumoniae</i> and the periodontal pathogens <i>Porphyromonas gingivalis</i> and <i>Actinobacillus actinomycetemcomitans</i> were measured. <i>Results:</i> In Finland 34.3% and in Russia 23.3% of the study population was atopic (p < 0.001). Seroprevalences to all these pathogens were significantly higher among the Russians. In multivariate logistic regression analysis, only <i>H. pylori</i> was inversely associated with atopy in Russia. A further stepwise analysis revealed that <i>H. pylori</i> alone can explain 32% of the difference in atopy between the countries, and <i>T. gondii, A. actinomycetemcomitans</i>, HSV and <i>C. pneumoniae</i> had a slightly additive effect, whereas, unexpectedly, seropositivity to HAV and, to a lesser extent, <i>P. gingivalis</i> had an opposite effect. The net result of the stepwise analysis showed that 44% of the difference in atopy between the countries could be explained by seropositivity to these seven pathogens. <i>Conclusions:</i> Seropositivity to select pathogens, particularly to <i>H. pylori</i>, could explain a substantial part of the difference in atopy prevalence between Finland and Russia. Exposure to HAV was not associated with protection against atopy in this adult population.