BackgroundCardiovascular disease (CVD) is a public health concern worldwide. Hypertensive heart disease is predominant in Nigeria. To effectively reduce CVD in Nigeria, the prevalence of, and factors associated with, pre-hypertension in Nigerian youth first need to be established.MethodsA locally-validated CVD risk factor survey was completed by 15–18 year olds in a rural setting in south-west Nigeria. Body Mass Index (BMI), waist-hip ratio and systolic and diastolic blood pressure was measured. Putative risk factors were tested in gender-specific hypothesized causal pathways for overweight/obesity, and for pre-hypertension.ResultsOf 1079 participants, prevalence of systolic pre-hypertension was 33.2 %, diastolic pre-hypertension prevalence approximated 5 %, and hypertension occurred in less than 10 % sample. There were no gender differences in prevalence of pre- hypertension, and significant predictors of systolic pre-hypertension (high BMI and older age) were identified. Considering high BMI, older age was a risk for both genders, whilst fried food preference was female-only risk, and low breakfast cereal intake was a male-only risk.ConclusionRural Nigerian adolescents are at-risk of future CVD because of lifestyle factors, and high prevalence of systolic pre-hypertension. Relevant interventions can now be proposed to reduce BMI and thus ameliorate future rural adult Nigerian CVD.Electronic supplementary materialThe online version of this article (doi:10.1186/s12872-015-0134-x) contains supplementary material, which is available to authorized users.