Intestinal parasitic infections have been considered a relevant public health problem due to the increased incidence worldwide. In developing countries, diarrhea and gastrointestinal symptoms cause impaired work capacity in adults and delayed rate growth in children. Enteric infections of unknown etiology can often lead to misdiagnosis, increased transmission, and morbidity. The aim of this study was to determine the prevalence of intestinal parasites in a young adult population and their pets. Stool samples from 139 university students and 44 companion animals were subjected to microscopy diagnosis using wet mounts, concentration by zinc sulphate flotation and staining techniques (Kinyoun and trichrome stain). Molecular diagnosis of protozoa was also performed by conventional PCR. The mean age was 24 years, 54% individuals were female, 46% were men, and 66% had at least one pet. The overall prevalence for at least one parasite was 74.8% and the rate of polyparasitism was 37.5%. Eighty-three patients (59.7%) were positive forBlastocystisspp., followed byCryptosporidiumspp. 24.5%,Endolimax nana13.6%,Entamoeba dispar/E.moshkovskii7.8% andGiardia intestinalis1.4%. Molecular diagnosis substantially improvedCryptosporidiumspp. andBlastocystisspp. detection and allowed to distinguishE.histolyticafrom commensals in theEntamoebacomplex. Student’s pets were also examined for parasitism. Samples from 27 dogs, 15 cats, one rabbit and one hen were analyzed, and parasites were detected in 30 (68.2%) as follows:Cryptosporidiumspp. (24)Giardiaspp. (4), hookworm (3),Endolimax nana(2) andToxoplasma gondii(1). Overall, university students showed high prevalence of parasitism and polyparasitism suggesting exposure to parasite infected animals and contaminated environments.Cryptosporidiumspp. was the predominant pathogen in human and domestic animals, and it was only detected by PCR, pointing out the need for sensitive tests in diagnosis and surveillance. Control strategies to prevent the effects of parasitic infections in young population should consider pets as reservoirs and transmission source.