The prevalence of hypertension in sub-Saharan Africa is increasing rapidly, and treatment remains challenging. Although the use of L-carnitine in treatment has received much attention, studies reporting on physiological L-carnitine levels in hypertensives are limited. Our aim was to determine physiological levels of L-carnitine and acylcarnitines in African and Caucasian men, and to investigate associations between ambulatory blood pressure (BP) and carnitine levels. Participants included 101 African and 101 Caucasian teachers. Ambulatory BP measurements were conducted, and L-carnitine and acylcarnitine levels determined. African men showed significantly higher systolic BP (p < 0.001), diastolic BP (p < 0.001) and L-carnitine levels (p = 0.01). In both ethnic groups, partial regression analyses revealed a positive association between BP and L-carnitine, although in Caucasians it was with systolic (r = 0.20, p = 0.045), and in Africans with diastolic BP (r = 0.23, p = 0.023). After adjusting for confounders, an independent positive association between systolic (R(2) = 0.37, β = 0.12, p = 0.041) and diastolic BP (R(2) = 0.39, β = 0.14, p = 0.018) and L-carnitine and long-chain acylcarnitines (R(2) = 0.38, β = 0.17, p = 0.005 and R(2) = 0.39, β = 0.15, p = 0.011) were found, independent of ethnicity. Physiological L-carnitine levels were not only higher in Africans than in Caucasians but also above the expected reference range. Despite promising results on L-carnitine (and its short-chain derivatives) in hypertension treatment regimens, our findings paradoxically show that elevated BP is significantly associated with higher physiological L-carnitine and long-chain acylcarnitine levels.