Nowadays, scientific studies are emerging on the possible etiological role of intestinal parasites in functional digestive disorders. Our study was carried out with healthy individuals (control group; n = 82) and symptomatic patients with lactose or fructose malabsorption, including positive (malabsorbers; n = 213) and negative (absorbers; n = 56) breath test, being analyzed for the presence of intestinal parasites. A high parasitic prevalence was observed in malabsorbers (41.8%), exclusively due to single-cell eukaryotes but not helminths. Giardia intestinalis was the predominant parasite in cases of abnormal absorption (26.5%), significantly associated with fructose malabsorption and doubling the probability of developing this pathology. Within controls, Blastocystis sp. (13.4%) was almost the only parasite, being the second among patients (12.6%), and Cryptosporidium parvum, the last species of clinical relevance, was detected exclusively in two malabsorbers (0.9%). The consumption of ecological food and professions with direct contact with humans arose as risk factors of parasitism. A diagnosis of carbohydrate malabsorption in adulthood is the starting point, making the search for the primary cause necessary. Accurate parasitological diagnosis should be considered another tool in the clinical routine for patients with recurrent symptoms, since their condition may be reversible with adequate therapeutic intervention.