Background Inadequate nutrition; neglected topical diseases; and insufficient water, sanitation, and hygiene (WASH) are interrelated problems in schools in low-income countries, but are not routinely tackled together. A recent three-year longitudinal study investigated integrated school health and nutrition approaches in 30 government primary schools in southern Ethiopia. Here, we report on baseline associations between sanitation, hookworm infection, anemia, stunting, and wasting. Methods In each school, the Schistosoma mansoni, S. haematobium, and soil-transmitted helminth infection intensities; blood hemoglobin concentrations; heights; and weights of approximately 125 students were assessed. Of these 125 students, approximately 20 were randomly selected for student WASH surveys. Of these 20, approximately 15 were randomly selected for household sanitation observations. School WASH was also assessed through a combination of observations and questions to the headteacher. Mixed-effects logistic regression was used to compare household sanitation with hookworm infection (the other parasites being much less prevalent); and hookworm infection with anemia, stunting, and wasting. Findings Blood, stool, and urine samples were provided by 3,729 children, and student WASH and household WASH surveys were conducted with 596 and 448 of these students, respectively. Hookworm, Ascaris lumbricoides, Trichuris trichiura, and S. mansoni infections had prevalences of 18%, 4.8%, 0.6%, and 0.3%, respectively, and no S. haematobium infections were found. Anemia, stunting, and wasting had prevalences of 23%, 28%, and 14%, respectively. No statistically significant associations were found between latrine absence or evidence of open defecation at home, and hookworm infection (adjusted odds ratio, OR = 1.28, 95% confidence interval, CI: 0.476–3.44; and adjusted OR = 1.21, 95% CI: 0.468–3.12; respectively); or between hookworm infection and anemia, stunting, or wasting (adjusted OR = 1.24, 95% CI: 0.988–1.57; adjusted OR = 0.992, 95% CI: 0.789–1.25; and adjusted OR = 0.969, 95% CI: 0.722–1.30; respectively). Conclusions In this setting, no statistically significant associations were found between sanitation and hookworm; or between hookworm and anemia, stunting, or wasting. More evidence on best practices for integrated school health interventions will be gathered from the follow-up surveys in this study., Author summary It is thought that inadequate sanitation may exacerbate hookworm transmission, and that hookworm infection may give rise to health problems including anemia, stunting, and wasting. Integrating monitoring of, and interventions against, these problems may yield significant cost savings. Such integrated interventions should be guided by both evidence of the relationships between the various health problems, and examples of optimally effective integration. Here, we present baseline findings from a three-year longitudinal study investigating combined school feeding; school water, sanitation, and hygiene (WASH); and deworming interventions in 30 primary schools in southern Ethiopia. In particular, we compare household sanitation, hookworm infection, and anemia, stunting, and wasting, in the schoolchildren. None of these associations were found to be statistically significant (although hookworm infection was associated with borderline statistically significantly higher odds of anemia; P = 0.06). The lack of significant associations may be due to the low intensities of the hookworm infections in this setting, poor conditions of latrines reducing their impact on hookworm transmission, and other factors such as malaria and inadequate diet causing anemia, stunting, and wasting.