The clinical and microbiological characteristics of super-infected hydatid cysts are described. In our cohort, 7.3% of 503 patients had a super-infected cyst. Four patients developed severe sepsis, and two of them died. Escherichia coli, viridans group streptococci, and Enterococcus species in liver cysts and Aspergillus fumigatus in lung cysts were the microorganisms most frequent involved.