Background Abnormalities in left ventricular (LV) structure and function are prevalent in patients on peritoneal dialysis (PD). The risk of cardiovascular mortality is also 10 – 20 times higher in PD patients than in age- and gender-matched healthy control subjects. Methods Echocardiography was performed annually or every 6 months for children on PD; the frequency was increased if the patient had hypertension or any heart problem. We retrospectively reviewed echocardiographic findings of these children (since February 2005) by chart review. The linear regression analysis of log(B-type natriuretic peptide, BNP) was performed to evaluate the association between serum BNP and cardiac parameters on echocardiography. Results We enrolled 52 patients and evaluated 169 echocardiographic findings in association with serum BNP levels. Systolic blood pressure (adjusted R2 = 0.321), diastolic blood pressure (adjusted R2 = 0.292), LV posterior wall thickness at diastole (0.058), LV posterior wall thickness at systole (0.038), LV internal diameter at diastole (0.177), LV internal diameter at systole (0.132), LV mass index (0.122), thickness of interventricular septum at diastole (0.035), the left atrial (LA) diameter (0.201), LA/aorta diameter ratio (0.113), lateral E/E’ (0.229), and lateral A'/E’ (0.149) showed positive correlation with log(BNP); conversely, LV fractional shortening (FS) (0.065), LV ejection fraction (0.082), right ventricular internal diameter at diastole (0.184), right ventricular fractional shortening (0.754), lateral S’ (0.179), and lateral E’ (0.161) showed negative correlation with log(BNP). Conclusions Routine measurement of serum BNP is recommended in children on PD to evaluate the risk of morphological and functional cardiac problems.