Background: Significant morbidity in children is associated with infectious diseases especially soil-transmitted helminth (STH) infections which are prevalent in sub-Saharan African countries. The objective of this study is to estimate the prevalence of STH and intestinal protozoa among schoolchildren in Lomé, Togo. Patients and Methods: In November 2013, in each of the five districts of the Lomé-commune region, thirty pupils per level of the third, fourth, fifth and sixth grades of five primary schools were included. Each child submitted a single stool sample that was analyzed by the Kato-Katz method for STH. In addition, stool samples of school children selected in third and sixth grades were examined by direct visualization using saline and Lugol's stain for intestinal protozoa. Results: A total of 2944 children were enrolled at 25 schools. The overall prevalence of STH at schools was 5.0% (range 1.5% to 8.6%), was higher in boys than girls, and increased with age and grade. Hookworm was the most prevalent species (3.4% of children surveyed). Intestinal protozoa were found in 52.2% (765/1465) of children tested and commensal amoebae represented 22.7% of these protozoa identified. Entamoeba histolytica/dispar/moshkovskii and Giardia intestinalis were identified in 2.3% and 11.5% of children, respectively. Co-infestation was noted in 1.