This paper investigates differences in the parasympathetically mediated heart rate response to head-up tilt in two populations of newborns. One group was unexposed to any drug during pregnancy, the other was exposed to both alcohol and smoking in utero. Four different estimates of vagal tone were calculated. These indexes quantify vagal tone magnitude in four different domains: time, frequency, complexity and phase. Control group (CG) results across all parameters show a consistent physiological response to an orthostatic tilt consistent with vagal withdrawal. On the other hand, infants in the exposed group (EG) did not express a decrease in vagal measures following tilt.