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Background: QUALMAT project aimed at improving quality of maternal and newborn care in selected health care facilities in three African countries. An electronic clinical decision support system was implemented to support providers comply with established standards in antenatal and childbirth care. Given that health care resources are limited and interventions differ in their potential impact on health and costs (efficiency), this study aimed at assessing cost-effectiveness of the system in Tanzania.Methods: This was a quantitative pre- and post- intervention study involving 6 health centres in rural Tanzania. Cost information was collected from health provider's perspective. Outcome information was collected through observation of the process of maternal care. Incremental cost-effectiveness ratios for antenatal and childbirth care were calculated with testing of four models where the system was compared to the conventional paper-based approach to care. One-way sensitivity analysis was conducted to determine whether changes in process quality score and cost would impact on cost-effectiveness ratios.Results: Economic cost of implementation was 167,318 USD, equivalent to 27,886 USD per health center and 43 USD per contact. The system improved antenatal process quality by 4.5% and childbirth care process quality by 23.3% however these improvements were not statistically significant. Base-case incremental cost-effectiveness ratios of the system were 2469 USD and 338 USD per 1% change in process quality for antenatal and childbirth care respectively. Cost-effectiveness of the system was sensitive to assumptions made on costs and outcomes.Conclusions: Although the system managed to marginally improve individual process quality variables, it did not have significant improvement effect on the overall process quality of care in the short-term. A longer duration of usage of the electronic clinical decision support system and retention of staff are critical to the efficiency of the system and can reduce the invested resources. Realization of gains from the system requires effective implementation and an enabling healthcare system.Trial Registration: Registered clinical trial at www.clinicaltrials.gov ( NCT01409824 ). Registered May 2009. [ABSTRACT FROM AUTHOR]