Intestinal disorders are a quite frequent occurrence in domestic cats younger than 1 year of age. Aim of the present study was to conduct a cross-sectional survey on the prevalence of enteric protozoan infections among cats clinically affected by intestinal disorders and to give a description of the clinical patterns. The study involved 92 kittens, less than 12 months old, belonging to cat shelters (n. 37) and private households (n. 55) and showing alterations of the macroscopic characteristics of the stools. Each animal was subjected to clinical examination and data collection. Individual faecal samples were collected during the visits. Each sample was examined by means of a flotation-centrifugation technique, processed for the copro-antigenic identification of Giardia duodenalis and Cryptosporidium spp. and tested for the detection of Tritrichomonas foetus by molecular tools. The results of the present survey showed that enteric protozoan parasitism is a condition frequently associated with intestinal disorders in cats under 1 year of age. Overall, 21.74% of the animals tested positive for at least one protozoan species. In the infected animals, the following parasites were identified: G. duodenalis (14.13%), Cystoisospora spp. (10.87%) and T. foetus (2.17%). Having an age less than 4 months and living in a shelter resulted prognostic for protozoan infections. Otherwise, clinical signs were not indicative, with the exception of haematochezia and steatorrhoea, for, respectively, Cystoisospora spp. and G. duodenalis infections. Given the limited number of T. foetus infections detected, further studies are necessary to confirm any consideration concerning this pathogen.