Long-term cardiac complications, occurring several years after completion of anticancer treatment, may develop from subclinical myocardial damage induced during cardiotoxic therapy. The aim of this study was to evaluate the usefulness of frequency-domain signal-averaged ECG analysis of the QRS complex for assessing the cardiotoxicity of anthracycline cytostatics. Altogether, 172 signal-averaged electrocardiography (SAECG) registrations were performed in 50 repeatedly evaluated oncologic patients. These registrations were performed 0.2-15 years after completion of anthracycline therapy for childhood cancer. The control group consisted of 120 healthy children and young volunteers; in 20 of these controls, SAECGs were performed repeatedly. Using gliding window fast Fourier transformation within the QRS complex, values area ratio (AR) 60-120 Hz/0-120 Hz were calculated in X, Y, and Z lead. Area ratio of patients after anthracycline therapy was significantly higher than those in control group in X lead. Differences in frequency content in the QRS complex between patients and controls might signal an initial stage of anthracycline-induced myocardial damage.