BackgroundMany small studies have been done in Honduras estimating soil-transmitted helminthiasis (STH) prevalence but a country-wide study was last done in 2005. The country has the highest burden of malaria among all Central American countries. The present study was done to estimate country-wide STH prevalence and intensity, malaria prevalence and nutritional status in school going children.Methods and FindingsA cross-sectional study was conducted following PAHO/WHO guidelines to select a sample of school going children of 3rd to 5th grades, representative of ecological regions in the country. A survey questionnaire was filled; anthropometric measurements, stool sample for STH and blood sample for malaria were taken. Kato-Katz method was used for STH prevalence and intensity and rapid diagnostic tests, microscopy, and polymerase chain reaction (PCR) were used for malaria parasite detection. A total of 2554 students were studied of which 43.5% had one or more STH. Trichuriasis was the most prevalent (34%) followed by ascariasis (22.3%) and hookworm (0.9%). Ecological regions II (59.7%) and VI (55.6%) in the north had the highest STH prevalence rates while IV had the lowest (10.6%). Prevalence of one or more high intensity STH was low (1.6%). Plasmodium vivax was detected by PCR in only 5 students (0.2%), all of which belonged to the same municipality; no P. falciparum infection was detected. The majority of children (83%) had normal body mass index for their respective age but a significant proportion were overweight (10.42%) and obese (4.35%).ConclusionsBiannual deworming campaigns would be necessary in ecological regions II and VI, where STH prevalence is >50%. High prevalence of obesity in school going children is a worrying trend and portends of future increase in obesity related diseases. Malaria prevalence, both symptomatic and asymptomatic, was low and provides evidence for Honduras to embark on elimination of the disease.