Coccidian oocysts were prevalent in nearly 100% of goats and sheep from various localities in Slovakia. In goats 4 Eimeria species were identified: E. ninakohlyakimovae (in kids 40%, in adult goats 51%), E. arloingi (in kids 43%, in adult goats 20%), E. alijevi (in kids 12%, in adult goats 21%) and E. hirci (in kids 3%, in adult goats 2%). In addition, 2-6% of coccidian oocysts were not speciated. The mean number of oocysts per gram of faeces (OPG) was 5853 +/- 12666 (min. 160 - max. 31920) in kids and 2365 +/- 4916 (min. 80 - max. 7920) in adult goats. In sheep 5 Eimeria species were identified: E. parva (in lambs 42%, in adult sheep 37%), E. ovinoidalis (in lambs 33%, in adult sheep 29%), E. crandallis (in lambs 14%, in adult sheep 19%), E. bakuensis (in lambs 6%, in adult sheep 6%), E. faurei (in lambs 3%, in adult sheep 4%); 2-5% of coccidian oocysts could not be classified. The mean OPG value was 11941 +/- 9048 (min. 2680 - max. 48880) in lambs and 5250 +/- 3412 (min. 880 - max. 12280) in adult sheep. In connection with the occurrence of pathogenic Eimeria species, the total counts of selected enterobacteriae in faeces of both goats and sheep were also evaluated. In spite of the fact that in kids the mean OPG numbers were lower, the values of total bacterial counts in their faeces were 1-2 orders of magnitude higher than in lambs. In comparison with lambs, organisms of kids are probably more susceptible to influence of pathogenic Eimeria species. The total counts of selected enterobacteria genera in goats and sheep with coccidiosis were higher than in control groups. These increased bacterial counts might be affected by impaired immunity of the host. Other factors as feeding, breeding conditions and management etc. may be also taken into consideration.