Abstract Background People living with HIV (PLHIV) are at increased risk for cardiovascular disease (CVD). In Sub-Saharan Africa, where a majority of PLHIV live, population-based data on major CVD events such as stroke and myocardial infarction are difficult and expensive to collect. The use of proxy measures of future CVD events that are easier to collect, could be a feasible way to better study CVD in such settings. This study aimed to determine the acceptability of incorporating ECG and arterial function measurements into a population-based cohort study and to assess the prevalence of ECG abnormalities and arterial stiffness. Methods A pilot study was conducted within the Rakai community cohort study in Uganda on two high-risk CVD groups; one determined by age (35-49) and Framingham CVD risk scores and the other by age alone (50+). Data on ECG, arterial function, blood pressure, and HIV status were collected. The acceptability of incorporating ECG and arterial function measurements was established as an acceptance rate difference of no more than 5% to blood pressure measurements. Results A total of 118 participants were enrolled, 57 PLHIV and 61 HIV negative. Both arterial function and ECG measurements were well accepted (2% difference), but the completeness of arterial function measurements captured was suboptimal (63%). Left ventricular hypertrophy (LVH) and arterial stiffness (> 10 m/s) were common in both PLHIV and HIV negative participants across the two high-risk populations. Prevalence rates ranged from 30% to 53% for LVH and 25% to 58% for arterial stiffness. Conclusions The incorporation of ECG and arterial function measurements into routine activities of a population-based cohort was acceptable. LVH and arterial stiffness were common in these high-risk for CVD populations, indicating the need for future research. The use of these proxy measures might be recommended when data on CVD events cannot be collected. Key messages It is acceptable to incorporate ECG and arterial function measurements into a population-based cohort in Uganda. High prevalence rates of LVH and arterial stiffness were found in people with high risk for CVD.