Introduction: Non-communicable diseases (NCDs) pose a significant health burden in India, with preventable risk factors contributing to their prevalence. Intergenerational inequities can exacerbate the transmission of health risks to further disadvantage vulnerable populations. Taking a life course perspective, this multi-generational cohort study aims to investigate behavioural, socio-ecological, and socio-economic determinants of growth and NCD risk, as well as healthcare access and utilization among rural households that include preadolescent children and their parents. Methods: The study is being implemented by Hirabai Cowasji Jehangir Medical Research Institute (HCJMRI) utilizing a prospective multi-generational cohort design to investigate NCD risk across 15 years. Data are being collected from 12 villages around Pune, Maharashtra, India. The primary population enrolled includes apparently asymptomatic (i.e., healthy) children aged 8 to 10 years and their parents. The sample size calculation (N=1300 children) for this longitudinal prospective cohort was driven by the primary objective of assessing trajectories of growth and NCD incidence across generations. A total of 2099 children aged 6 to 10 years have been screened since April 2022, of whom 1471 have been found to be eligible for inclusion in the study. After obtaining informed consent from parents and their children, comprehensive bi-annual data are being collected from both children and parents, including clinical, behavioural, healthcare access and utilization as well as socio-ecological and socio-economic determinants of health. Participants (children and their parents) are being enrolled through household visits, and by arranging subsequent visits to the primary health facility of HCJMRI. Clinical assessments include anthropometric measurements, blood samples for a wide range of NCD indicators, bone health, and muscle function. The long-term data analysis plan includes longitudinal modeling, time-series analyses, structural equation modeling, multilevel modeling, and sex and gender-based analyses. Ethics approval has been obtained from the institutional ethics committee, the Ethics Committee Jehangir Clinical Development Centre Pvt Ltd. Written informed consent is obtained from adults and written informed assent from children. Discussion: As of May 2023, 378 families from 10 villages have been enrolled, including 432 preadolescents and 756 parents. Preliminary results not only highlight the double burden of malnutrition in the cohort with undernutrition and overweight/obesity coexisting among children and parents, respectively but also identify high rates of diabetes and hypertension among adults in rural areas. Findings can inform the development of targeted interventions to reduce NCDs, address intergenerational health inequities, and improve health outcomes in vulnerable populations.