This study aimed to explore secondary school students' conceptual understanding of the selected concept of genetics including cell division, fertilization and reproduction and genetic relationship between cells within an individual. Another aim was to explore the difference in conceptual understanding of the children across government and private schools. A total of 370 children of grade nine were recruited through multistage cluster sampling approach from both government (n=182) and private (n=188) schools from district Ghanche and Skardu in Gilgit-Baltistan. Genetic Conception Assessment (GCA) tool adapted from a previous study was administered to explore children's conceptions about selected topics of genetics. The content validity of GCA was established through expert review. Internal consistency of the assessment tool was found to be satisfactory (0.78). Results demonstrated that children scored only 34% of the total score exhibiting a weak conceptual understanding in selected concepts of genetics. On average children performance for MCQs was comparatively better (50% of the total marks). However, children's achievement remained marginal (13% of the total marks) in CRQs which aimed to identify some of the prevailing misconceptions. Results followed almost the same pattern for the three concepts focused in GCA-cell division, fertilization and reproduction, and ceil focused in GCA. A comparison of GCA scores across school system showed that the children from private schools outperformed their government counterparts (p<0.001, r=0.58). Similarly, private school children maintained their better performance both in MCQs (p<0 001 r=0.46), CRQs (p<0.001, r=0.58) and across the sections of GCA. This study provides significant insight into an under-researched area. Keeping the results of the study in view, the role of quality instruction in developing conceptual understanding of students at secondary level could be emphasized. The adapted 16 item GCA questionnaire would make a valuable contribution in indigenous literature. Those who want to take the same line of inquiry can use this tool to conduct large scale studies.