Magnetocardiographic recordings from a fetus at 34 weeks' gestation with a complex heart malformation revealed an unusual fetal arrhythmia, where the rhythm was observed to alternate between extended periods of sinus and junctional rhythms. Fetal heart rate measurement showed that the junctional rhythm was strongly associated with respiratory arrhythmia. We hypothesize that changes in autonomic balance due to the onset and cessation of fetal breathing movements were largely responsible for the rhythm alternations. To our knowledge this is the first report of a fetal junction rhythm and the first observation of fetal respiratory arrhythmia during nonsinus rhythm.