Giardia duodenalis prevalence is commonly as high as soil-transmitted helminths (STH), nevertheless is not considered for large-scale chemotherapy through mass drug administration (MDA) due to its short incubation period and frequent reinfections, its control being associated to improving access to water and sanitation. A study enrolling 444 children attending preschools was conducted in May 2011 during a deworming campaign. Faecal samples were obtained and analysed through microscopy of wet mounting and after Kato–Katz and formol-ether concentration techniques. The majority of children were infected with at least one pathogenic parasite (86.7%, 385 of 444). Ascaris lumbricoides and Trichuris trichiura (56.3%, 250 of 444 and 52.5%, 233 of 444, respectively) were the most frequent parasites followed by G. duodenalis infecting 41.7% (185 of 444) of the children. The present work aimed at obtaining updated information concerning intestinal parasite infections in children attending preschools in São Tomé and Príncipe and to contribute for the adequate management of the enteric infections.