BackgroundIntestinal parasitic infections in dogs and cats represent a significant clinical challenge and pose relevant zoonotic risks to public health. Epidemiological data on Portuguese companion animals remain scarce, with limited sample sizes and geographic coverage, leaving key gaps in understanding parasite prevalence and associated risk factors.MethodsThis cross-sectional epidemiological study investigated the prevalence and associated risk factors of intestinal parasitism in 363 dogs and 345 cats, sampled from companion, breeding, shelter, and stray populations between November 2022 and April 2025. A total of 708 fecal samples were analyzed using coprological techniques (flotation and sedimentation), Giardia immunochromatographic test, and modified Ziehl-Neelsen staining.ResultsOverall, 41.6% of dogs were positive for intestinal parasites, with protozoa and monoparasitism (61.2%) predominating. Giardia lamblia was the most frequently detected (44.7%), followed by Ancylostomatidae (16.5%), Cystoisospora spp. (15.4%), Toxocara canis (14.9%), Trichuris vulpis (4.3%), Cryptosporidium spp. (3.2%), and Toxascaris leonina (1%). Among cats, 42.6% tested positive, exhibiting greater parasite diversity, with a predominance of helminths and a higher occurrence of polyparasitism (116/211; 55%). The most prevalent parasite was Toxocara cati (30.3%), Ancylostomatidae (27.5%), Cystoisospora spp. (18%), Aelurostrongylus abstrusus (10.4%), G. lamblia (7.2%), and Cryptosporidium spp. (3.3%). Less frequent parasites included Dipylidium caninum, Mesocestoides spp., Cystoisospora rivolta, Toxoplasma gondii-like oocysts, and Troglostrongylus. Stray and shelter animals had significantly higher infection risks (OR = 2.3 for dogs; OR = 4.5 for cats). Age, abnormal fecal consistency, and seasonality were additional factors significantly associated with parasite positivity.ConclusionTaken together, the detection of intestinal parasites in 41.6% of dogs and 42.6% of cats highlights a substantial burden, with parasites of zoonotic potential accounting for 73.9% of all positive results (295/399). These high rates point to critical gaps in preventive care among companion animal populations, underscoring the urgent need for strengthened surveillance, targeted treatment protocols, and enhanced public health education to reduce parasite burdens and mitigate zoonotic risks in Portugal.