Most high-yielding cassava cultivars have high cyanogenic glycoside (CNglcs) content in their roots and the CNglcs content of < 50 ppm in fresh root is considered safe for consumption. The root yield and CNglcs content which are agronomic traits involving several genes and environmental interactions can be evaluated only during the harvest time. In this study, 83 breeding lines and parents were evaluated for the variation and correlation between root yield and CNglcs content with 17 agronomic traits: root weight, leaf weight, stem weight, starch content, harvest index, root number, plant type, plant height, the first branch height, cyanide-equivalent contents in root and in leaf, chlorophyll content, carotenoid contents in leaf and in root, and cassava bacterial blight, fibrous and tuberous root-knot symptom scorings that may affect root yield and CNglcs content. The multiple regression and path analysis indicated that: a) harvest index, leaf weight and stem weight, and b) stem weight, starch content, CNglcs content in leaf, the first branch height and leaf weight could produce root weight with predicted R² = 86.03 and 47.05%, respectively. Also, a) chlorophyll content, CNglcs content in leaf, and root-knot symptom scoring, and b) carotenoid content in leaf and CNglcs content in leaf could be used in screening for low CNglcs content in root with predicted R² = 52.20 and 55.06%, respectively. However, CNglcs content in leaf and root did not show any correlation with cassava bacterial blight and fibrous root-knot symptom scorings. Further evaluation and trial in other locations are required for the verification.