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Background: Guatemala is presently engaged in the Central America Initiative to interrupt Chagas disease transmission by reducing intradomiciliary prevalence of Triatoma dimidiata, using targeted cross-sectional surveys to direct control measures to villages exceeding the 5% control threshold. The use of targeted surveys to guide disease control programs has not been evaluated. Here, we compare the findings from the targeted surveys to concurrent random cross-sectional surveys in two primary foci of Chagas disease transmission in central and southeastern Guatemala. Methodology/Principal Findings: Survey prevalences of T. dimidiata intradomiciliary infestation by village and region were compared. Univariate logistic regression was used to assess the use of risk factors to target surveys and to evaluate indicators associated with village level intradomiciliary prevalences >5% by survey and region. Multivariate logistic regression models were developed to assess the ability of random and targeted surveys to target villages with intradomiciliary prevalence exceeding the control threshold within each region. Regional prevalences did not vary by survey; however, village prevalences were significantly greater in random surveys in central (13.0% versus 8.7%) and southeastern (22.7% versus 6.9%) Guatemala. The number of significant risk factors detected did not vary by survey in central Guatemala but differed considerably in the southeast with a greater number of significant risk factors in the random survey (e.g. land surface temperature, relative humidity, cropland, grassland, tile flooring, and stick and mud and palm and straw walls). Differences in the direction of risk factor associations were observed between regions in both survey types. The overall discriminative capacity was significantly greater in the random surveys in central and southeastern Guatemala, with an area under the receiver-operator curve (AUC) of 0.84 in the random surveys and approximately 0.64 in the targeted surveys in both regions. Sensitivity did not differ between surveys, but the positive predictive value was significantly greater in the random surveys. Conclusions/Significance: Surprisingly, targeted surveys were not more effective at determining T. dimidiata prevalence or at directing control to high risk villages in comparison to random surveys. We recommend that random surveys should be selected over targeted surveys whenever possible, particularly when the focus is on directing disease control and elimination and when risk factor association has not been evaluated for all regions under investigation. Author Summary: Chagas disease is a vector-borne parasitic zoonosis endemic throughout South and Central America and Mexico. Guatemala is engaged in the Central America Initiative to interrupt Chagas disease transmission. A major strategy is the reduction of Triatoma dimidiata domiciliary infestations through indoor application of residual insecticides. Successful control of T. dimidiata will depend on accurate identification of areas at greatest risk for infestation. Initial efforts focused primarily on targeted surveys of presumed risk factors and suspected infestation to define intervention areas. This policy has not been evaluated and might not maximize the effectiveness of limited resources if high prevalence villages are missed or low prevalence villages are visited unnecessarily. We compare findings from the targeted surveys to concurrent random surveys in two primary foci of Chagas disease transmission in Guatemala to evaluate the performance of the targeted surveys. Our results indicate that random surveys performed better than targeted surveys and should be considered over targeted surveys when reliability of risk factors has not been evaluated, identify useful environmental factors to predict infestation, and indicate that infestation risk varies locally. These findings are useful for decision-makers at national Chagas Disease control programs in Central America, institutions supporting development efforts, and funding agencies. [ABSTRACT FROM AUTHOR]