Background Malnutrition is a public health problem, but outside the theoretical framework, little is known about the concrete intergenerational effects of malnutrition. Objective The objective of this study is to compare the nutritional status and health indicators of school children born to mothers who were treated for severe acute malnutrition (SAM). Methodology The study took place in Miti-Murhesa health zone in the Democratic Republic of Congo. This is a cohort study assessing the nutritional and health status of school children born to mothers who had been treated for SAM, based on WHZ or edema, in Lwiro hospital between 1988–2002 compared to children born to mothers who were not exposed to SAM. Stunting and thinness were evaluated by Height for Age Z-score (HAZ) and Body Mass Index by Age criteria (BMIAZ) respectively. On admission, blood samples were taken to assess anemia, HIV serology, hemogram and others biological indicators. Stool’s examinations were conducted by using Olympus optical microscope. Parametric and non-parametric tests were applied to compare the different variables in two groups. Results We identified 106 children aged 5–16 years (103 exposed and 58 unexposed) and we received 83.5% and 91.4% children respectively for anthropometric parameters. The mean of age was 7.9 ± 2.4 year in exposed group and 7.4 ± 2.1 year in unexposed group (p = 0.26). The prevalence of stunting was 68.3% in the exposed group and 67.3% in the unexposed group (p = 0.90). The prevalence of thinness was 12.8% in the exposed group and 9.6% in the unexposed group (p = 0.57). The biological profile (glycemia, urea, creatinine and hemogram) and the prevalence of intestinal parasites were similar in the two groups. Conclusion In this sample, in a malnutrition-endemic area, there was no statistically significant difference in nutrition and health indicators between school children born to mothers exposed to SAM and their community controls.