Samples of excrements for parasitological investigation were obtained in two year period 2011 and 2012 on three sheep farms and two goat farms in South Bohemia (a farm conventional, an organic and converting to an organic farming system). A total of 400 samples were examined using four parasitological methods. Thirteen species of gastrointestinal nematodes and one species of Protozoa were recovered. In farms Coccidia Eimeria spp. was the most diagnosed. Results revealed that goats were 1,8 times more often infected with parasites than sheep (x2 = 6,274; d. f. = 1; p = 0, 00576; OR = 1,82). Animals younger 6 months were 3 times more often infected with Eimeria than older ones (x2 = 17,174; d. f. = 1; p = 0,00003; OR = 3,16). Goats were 11 times more often infected with parasites in winter than sheep (x2 = 5,8174; d. f. = 1; p = 0,0050; OR = 10,78). Goats were 2 times more often infected with lungworm infection than sheep (x2 = 8,407; d. f. = 1; p = 0,0019; OR = 1,99). A statistically significant difference in infectious contamination between conventional and an organic system bred animals was not discovered (x2 = 0,0145; d. f. = 1; p = 0,452; OR = 1,05).