In Italy, the limited resources and the large number of cats living in feline shelters may facilitate the spread of parasite infections that may affect the health of cats and expose shelter workers and adoptive owners to zoonosis. Prevalence and risk factors of potential zoonotic and host-specific gastrointestinal parasite infections were assessed in cats living in public and private shelters of central Italy. Individual fecal samples were examined macroscopically and then screened microscopically by fresh and Lugol stained fecal smears and by flotation and the Baermann tests. A commercial rapid immune-chromatographic assay was used to detect Giardia duodenalis and Cryptosporidium spp. All animals were clinically examined to evaluate presence of clinical signs compatible to parasitic infections. Data were statistically analysed by multivariate analysis with logistic regression and chi square testing for bivariate analysis. The overall prevalence of gastrointestinal parasites in the shelter cats surveyed was 22% (29/132), with 26/132 (19.7%) of the animals infected with potentially zoonotic organisms. Upon statistical analysis, parasite infections were identified in significantly more cats younger than 18 months of age (p <0.05), and most often associated with the presence of compatible clinical signs (p <0.05). A higher prevalence of protozoan infections (18.1%, 24/132) than of helminth infections (12.9%, 17/132) was observed. Identified parasites were Giardia duodenalis (10.6%, 14/132), Toxocara cati (9%, 12/132), Cystoisospora felis (3%, 4/132), Cystoisospora rivolta (2.3%, 3/132), hookworms (2.3%, 3/132), Cryptosporidium spp. (1.6%, 2/132), Aonchotheca putorii (0.75%, 1/132), Tritrichomonas foetus (0.75%, 1/132) and Strongyloides sp. (0.75%, 1/132). Co-infections were identified in the 7.6% of animals surveyed. Results obtained from this study indicate high gastrointestinal parasite risk to shelter cats and public health in the examined areas and suggest the need for more effective control measures in shelters surveyed.