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Background Toxoplasma gondii is found worldwide, and consumption of undercooked meat is considered a significant risk factor for human infections. In Denmark, little is known about the distribution of T. gondii , but a recent study revealed a seroprevalence of 34% in Danish indoor sows. The present cross-sectional study aimed to investigate the role of mice for the transmission of T. gondii in Danish indoor sow herds. Results In total, 56 sow herds were visited, 137 mice were caught by snap traps from 32 farms, and 52 cat faecal samples were collected from 22 farms. Eight percent of the mice were positive for T. gondii DNA, representing 11% of the farms. Significant associations were found between the presence of T. gondii -positive mice and both open feed systems (P= 0.041) and extra rodent control on the farm (P= 0.024). All cat faecal samples were deemed negative for T. gondii by light microscopy examination and real-time polymerase chain reaction analysis. Conclusion Mice captured inside Danish sow herds were found to be infected with T. gondii and may thus contribute to the transmission of T. gondii to sows, which may explain the high seroprevalence found in Danish pigs.