A congenital heart disease monitor utilizes a sensor capable of emitting multiple wavelengths of optical radiation into a tissue site and detecting the optical radiation after attenuation by pulsatile blood flowing within the tissue site. A patient monitor is capable of receiving a sensor signal corresponding to the detected optical radiation and calculating at least one physiological parameter in response. The physiological parameter is measured at a baseline site and a comparison site and a difference in these measurements is calculated. A potential congenital heart disease condition in indicated according to the measured physiological parameter at each of the sites or the calculated difference in the measured physiological parameter between the sites or both.