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A zoonosis called toxoplasmosis, which is caused by the protozoon Toxoplasma gondii, occurs worldwide. The prevalence of Toxoplasma infection varies in different populations, probably due to differences in exposure to Toxoplasma oocysts deposited in the environment by cats, different eating habits, hygiene standards and differences in climatic conditions and geographical location with respect to altitude. The aim of this study was to investigate whether the epidemiology of toxoplasmosis among pregnant women in two parts of Slovenia depends on different climatic conditions and different geographical locations. From 1 January 1999 to the end of 2003, 7,134 pregnant women from the littoral area of the Adriatic coast were serologically examined using enzyme immunoassay for Toxoplasma IgG antibodies and compared to 8,162 pregnant women from the continental central part of Slovenia who were serologically tested for Toxoplasma infection. In the Primorska region, where the weather is warm, dry and windy, and has a mild coastal climate without snow in winter, among 7,134 pregnant women 4,711 were Toxoplasma negative and 2,185 (31%) Toxoplasma positive; 95% CI (30%, 32%). In the continental area, where the climate is more humid, with higher rainfall and colder winters with snow, among 8,162 pregnant women’s sera, 4,922 were Toxoplasma negative and 3,240 (40%) Toxoplasma positive; 95% CI (39%, 41%). Statistically significant Toxoplasma positivity found among pregnant women in two areas of Slovenia (p < 0.0001) suggests that environmental conditions may affect the viability of the Toxoplasma oocysts and thus not only modulate the risk of Toxoplasma ingestion with soil, but also indirectly affect disease transmitted via different types of infected meat in these areas.