Relationships between the atria and the ventricles are commonly described in terms of either atrioventricular (AV) alignments (or connections) or AV situs (i.e., the type of atrial situs and the type of ventricular situs or ventricular loop). With either method of analysis, only one type of AV relationship (situs or alignment) is diagnosed specifically and is considered to be predictive of the other type of AV relationship. The two-dimensional echocardiographic characteristics of two patients with incongruent AV situs and alignments are described for the first time. Patient 1 had situs solitus of the viscera and atria (S), ventricular D-loop (D), and solitus normally related great arteries (S), or (S,D,S) segmental combination with concordant AV situs. However, the right-sided right atrium drained into the inferior and right-sided left ventricle, and the left-sided left atrium drained into the superior and left-sided right ventricle. Hence AV alignment discordance was present. Patient 2 had visceroatrial situs solitus (S), ventricular D-loop (D), and double-outlet right ventricle with a rightward aortic valve (D), or (S,D,D) segmental set (AV situs concordance). Similar to patient 1, AV alignment discordance was demonstrated. In both patients the diagnosis was established by two-dimensional echocardiography and subsequently confirmed by cardiac catheterization. The key to accurate echocardiographic diagnosis of this congenital heart disease was independent analysis of the AV alignments and the segmental situs of the three main cardiac segments. This diagnosis was determined by scanning from the parasternal, subxiphoid, and apical windows.(ABSTRACT TRUNCATED AT 250 WORDS)