The effect of alcohol exposure and hypoxia on the development of heart rate and heart inter-beat interval (IBI) variability was studied in preweanling rats. Rats were artificially reared from postnatal day (PD) 4 through 12 and either exposed to alcohol (5 g/kg/day) or hypoxia (2-15-min episodes/day) from PD 4 to 10. Control groups consisted of artificially reared and normally reared rats not exposed to alcohol or hypoxia. The heart rate and respiration was recorded for 20-min sessions every other day from PD 5 through 21. Inter-beat intervals and measures of their variability caused by respiratory sinus arrhythmia (RSA) were computed from the recordings. There was a steady decline in average IBI across this age range. There was little change in RSA from PD 5 to 15, followed by a large increase in RSA level from PD 15 to 21. The alcohol- and hypoxia-exposed rats showed significantly less increase in RSA level on PD 19 and 21. Large bradycardias occurred in all groups on PD 5, 9, and 17, and were more prevalent in rats exposed to alcohol or hypoxia. These data suggest that neural control of the chronotropic functions of the heart undergoes major changes in the late preweanling stage, and the changes in neural control are slowed by hypoxia or alcohol exposure during the early postnatal period.