Intestinal protozoa are ubiquitous parasitic species in carnivores, some of them with a significant zoonotic potential. Little is known on their prevalence in Romanian shelter dogs. Therefore, an epidemiological study was carried out in order to assess the occurrence and prevalence of digestive protozoa infections in shelter dogs, in South-eastern Romania. Dogs (n=420) originating in four shelters, one in Bucharest (n=105) and three from two neighbouring counties, two in Ilfov (n=166) and one in Giurgiu (n=149), were included in the study. Dogs were of mixed breed, aging from two months to 16 years (average=4.8 years; SD=3.8). To assess the risk factors for protozoan infections, animals were categorized in three age groups: <4 months, 4-12 months and >12 months. Fresh faecal samples collected from individual animals have been subjected for parasitological examination. Overall, 54.05% (95% CI: 49.14-58.89) of the animals were found positive for at least one parasitic species, protozoan and/or helminths. 11.9% of the dogs were positive for protozoa infections, as follows: 8.57% (36/420) for Isospora spp. and 3.33% (14/420) for Giardia duodenalis. Infection with Isospora showed a higher and statistically significant prevalence of 40.9% in the age group up to 4 months comparing with the other two age groups in which prevalence of 19.64% and 2.19%, respectively, was registered. The prevalence of G. duodenalis infection among these age groups varied from 5.36% to 3.44%. Of the 36 Isospora- and 14 Giardia-positive animals, 21 and 5 respectively were single infections, while 15 and 9, respectively, has mixed infections with one (n=5 and n=6), two (n=8 and n=2) or three (n=2 and n=1) different helminth species, as follows: Ancylostoma caninum, Toxocara canis, Toxascaris leonina, Trichuris vulpis, Dipylidium caninum. These findings show the occurrence and epidemiology of protozoa infections and a high diversity of parasitofauna in shelter dogs, including species with zoonotic potential emphasizing the urgent need for appropriate measure to be taken for the parasitological control.