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<p>Abstract</p> <p>Background</p> <p>Despite three decades of prenatal screening program for toxoplasmosis in Austria, population-based estimates for the incidence of maternal infections with <it>Toxoplasma gondii </it>during pregnancy are lacking. We studied the incidence of primary maternal infections during pregnancy in the Federal State of Upper Austria.</p> <p>Methods</p> <p>Screening tests for 63,416 women and over 90,000 pregnancies (more than 84.5% of pregnancies in the studied region) in the time period between 01.01.2000 and 31.12.2007 were analysed. The incidence of toxoplasmosis was estimated indirectly by binomial and directly by interval censored regression.</p> <p>Results</p> <p>During the studied period, 66 acute infections (risk of 0.07% per pregnancy) were detected, but only 29.8% of seronegative women were tested at least three times during their pregnancies. The seroprevalence of <it>Toxoplasma </it>antibodies among all tested women was 31%. Indirectly estimated incidence (from differences in prevalence by age) was 0.5% per pregnancy, while directly estimated incidence (interval censored regression) was 0.17% per pregnancy (95% confidence interval: 0.13-0.21%).</p> <p>Conclusions</p> <p>Calculating incidence from observed infections results in severe underreporting due to many missed tests and potential diagnostic problems. Using statistical modelling, we estimated primary toxoplasmosis to occur in 0.17% (0.13-0.21%) of all pregnancies in Upper Austria.</p>