Background: Coxiella burnetii is the etiological agent of Q fever, a zoonosis afecting many animal species including sheep and goats. The aims of this study were to evaluate the shedding of Coxiella burnetii in small ruminant herds and to identify the pathogen’s genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods. Results: Overall, 165 samples from 43 herds of goats and 9 focks of sheep were collected including bulk tank milk (BTM), individual milk samples, vaginal swabs, tissue sections from stillborn kids, feces and placentas. These were tested by real-time PCR targeting the IS1111 element. C. burnetii infection was confrmed in 51.16% of the herds of goats and 22.2% of the focks of sheep. Six out of nine samples originating from goats were successfully genotyped using the MLVA method. The presence was confrmed of two widely distributed MLVA genotypes (I and J) and genotype PL1 previously reported only in cattle. Only one sequence type (ST61) was identifed; however, the majority of specimens represented partial STs and some of them may belong to ST61. Other partial STs could possibly be ST74. Conclusion: This study confrmed the relatively common occurrence of Coxiella burnetii in small ruminant herds in Poland. Interestingly, all genotyped samples represent cattle-associated MLVA genotypes.