The objectives of this study were to investigate left ventricular (LV) function, aortic dilation, and atherosclerosis in children with mildly deteriorated isolated bicuspid aortic valve (BAV) function using echocardiographic studies and biochemical markers of atherosclerosis and to correlate results with normal children. Biochemical analyses indicating cardiovascular risk of atherosclerosis and vascular changes in the aorta in relation to BAV were performed in 41 children aged 5–15 years old with isolated BAV and in 25 children with tricuspid aortic valves. Evaluations of aortic valve structures and functions; examinations of the LV M-mode and ascending aorta Doppler; and measurements of the LV Tei index (MPI), propagation velocity, ascending aorta at four levels, and carotid intima–media thickness (CIMT) were performed. There were no statistically significant differences in CIMTs, plasma matrix metalloproteinase-9, tissue metalloproteinase inhibitor-1 levels, or other biochemical parameters indicating cardiovascular risk or atherosclerosis between study and control groups. Deterioration of LV function, which could not be seen with M-mode echocardiography, was evident by MPI. MPI values in the study versus control groups were 0.46 ± 0.080 versus 0.40 ± 0.086 (p < 0.05). Diameters of the aorta in the study and control groups were 19.7 ± 4.7 and 17.2 ± 2.8 mm (p < 0.05) at the sinotubular junction level and 20.6 (14.4–40.5) and 18.3 (12.4–24) mm at the ascending aorta level (p < 0.05). Increased aortic valve insufficiency was related to increased aortic diameter. No sign of atherosclerosis was detected in children with BAV. Deterioration of LV function was seen using MPI, and aortic dilation was related to the severity of aortic valve insufficiency.