A number of physiological studies, published over the last 10 years, have investigated the links between prone sleeping and sudden infant death syndrome (SIDS). This review evaluates those studies and derives an overview of the different affects of sleeping prone or supine in infancy. Generally, compared with the supine, the prone position raises arousal and wakening thresholds, promotes sleep and reduces autonomic activity through decreased parasympathetic activity, decreased sympathetic activity or an imbalance between the two systems. In addition, resting ventilation and ventilatory drive is improved in preterm infants, but in older infants (>1 month), there is no improvement in ventilation, and in 3-month-old infants, the position is adverse in terms of poorer ventilatory drive (in active sleep only). The majority of findings suggest a reduction in physiological control related to respiratory, cardiovascular and autonomic control mechanisms, including arousal during sleep in the prone position. Since the majority of these findings are from studies of healthy infants, continued reinforcement of the supine sleep recommendations for all infants is emphasized.