We examined the association between heart rate variability (HRV) and duration of type 2 diabetes among 155 female and 106 male subjects: mean+/-SD for duration=49.6+/-65.6 and 57.3+/-77.1 months, respectively, p=0.38. Among males, duration of diabetes was independently and inversely associated with vagal-heart rate modulation (high frequency (HF) power, 0.15-0.40 Hz, standardised ss = -0.32, p=0.001; root mean square of successive differences between R-R intervals, ss = -0.26, p=0.006) and total R-R variability (standard deviation of normal R-R intervals, ss = -0.36, p=0.001); but not among females (p> or =0.80 for each HRV index). In contrast, HF was inversely associated with age of diabetes diagnosis (ss = -0.16, p=0.04) and 10-year absolute risk for coronary heart disease (ss = -0.16, p=0.04) among female subjects. Longitudinal research is needed to establish whether risk factors for early cardiac autonomic impairment differ among men and women with type 2 diabetes.