In this study, a simple and efficient diagnostic system, which adopts a novel methodology consisting of principal component analysis (PCA)-based feature generation and ellipse models-based classification criterion, is proposed for the diagnosis of a ventricular septal defect (VSD). The three stages corresponding to the diagnostic system implementation are summarized as follows. In stage 1, the heart sound is collected by 3M-3200 electronic stethoscope and is preprocessed using the wavelet decomposition. In stage 2, the PCA-based diagnostic features, [[Formula: see text]], are generated from time-frequency feature matrix ([Formula: see text]). In the matrix TFFM, the time domain features [Formula: see text] are firstly extracted from the time domain envelope [Formula: see text] for the filtered heart sound signal [Formula: see text], and frequency domain features, [Formula: see text], are subsequently extracted from a frequency domain envelope ([Formula: see text]) for each heart sound cycle automatically segmented via the short time modified Hilbert transform(STMHT). In stage 3, support vector machines-based classification boundary curves for the dataset [Formula: see text] are first generated, and least-squares-based ellipse models are subsequently built for the classification boundary curve. Finally, based on the ellipse models, the classification criterion is defined for the diagnosis of VSD sounds. The proposed diagnostic system is validated by sounds from the internet and by sounds from clinical heart diseases. Moreover, comparative analysis to validate the usefulness of the proposed diagnostic system, mitral regurgitation and aortic stenosis sounds are used as examples for detection. As a result, the higher classification accuracy, which is achieved by this study compared to the other methods, is [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] for diagnosing small VSD, moderate VSD, large VSD and normal sounds, respectively.