Promoting HIV medication adherence is basic to HIV/AIDS clinical care and reducing transmission risk and requires sound assessment of adherence and risk behaviors such as substance use that may interfere with adherence. The present study evaluated the utility of a telephone-based Interactive Voice Response self-monitoring (IVR SM) system to assess prospectively daily HIV medication adherence and its correlates among rural substance users living with HIV/AIDS. Community-dwelling patients (27 men, 17 women) recruited from a non-profit HIV medical clinic in rural Alabama reported daily medication adherence, substance use, and sexual practices for up to 10 weeks. Daily IVR reports of adherence were compared with short-term IVR-based recall reports over 4- and 7-day intervals. Daily IVR reports were positively correlated with both recall measures over matched intervals. However, 7-day recall yielded higher adherence claims compared to the more contemporaneous daily IVR and 4-day recall measures suggestive of a social desirability bias over the longer reporting period. Nearly one-third of participants (32%) reported adherence rates below the optimal rate of 95% (range=0-100%). Higher IVR-reported daily medication adherence was associated with lower baseline substance use, shorter duration of HIV/AIDS medical care, and higher IVR utilization. IVR SM appears to be a useful telehealth tool for monitoring medication adherence and identifying patients with suboptimal adherence between clinic visits and can help address geographic barriers to care among disadvantaged, rural adults living with HIV/AIDS.