Parasitic agents are a common cause of diarrhea in dogs and cats and, thus, determining their prevalence is essential to establish preventive and control measures. This retrospective study examined the fecal tests records from 1111 dogs and 203 cats with diarrhea submitted to a diagnostic laboratory in the city of Medellin between January and May 2018. The detection of parasites was carried out by direct smears and simple flotation methods. Parasitic organisms were detected in feces from 464 (41.7%) dogs and 96 (47.3%) cats. In order of decreasing prevalence, the parasites detected in dogs were: Giardia intestinalis (13%), ancylostomids (12.6%), Entamoeba spp. (6.1%), coccidian oocysts (5.8%), Toxocara spp. (5.6%) and Dipylidium caninum (1.3%). In cats, the prevalence was: Giardia intestinalis (20%), coccidian oocysts (8.9%), Entamoeba spp. (7.9%), ancylostomids (6.4%), Toxocara spp. (2.5%) and Dipylidium caninum (2%). Age, but not gender, was a predisposing factor, as puppies and kittens had significantly higher infection rates that older age categories. The majority of Giardia intestinalis positive cases occurred in puppies (109/145, 75.2%) and kittens (19/36, 52.8%), making this parasite the most prevalent in amongst animals with diarrhea. Out of 117 positive infections in the adult dog population, ancylostomids accounted for 56 cases (47.9%) and was the most common parasite in this age group. In conclusion, although these results do not imply a cause and effect relationship, they are an estimate of the type of parasites that may be most commonly associated with diarrhea in dogs and cats. The lower diagnostic sensitivity of the traditional methods used here as compared to more contemporary techniques like fecal flotation with centrifugation and PCR, may have underestimated the actual prevalence and diminished the detection of coinfections. Future studies should aim to have diagnostic panels that also screen for other enteric pathogens, including bacterial and viral agents.