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Background Because the success of deworming programs targeting soil-transmitted helminths (STHs) is evaluated through the periodically assessment of prevalence and infection intensities, the use of the correct diagnostic method is of utmost importance. The STH community has recently published for each phase of a deworming program the minimal criteria that a potential diagnostic method needs to meet, the so-called target product profiles (TPPs). Methodology We compared the diagnostic performance of a single Kato-Katz (reference method) with that of other microscopy-based methods (duplicate Kato-Katz, Mini-FLOTAC and FECPAKG2) and one DNA-based method (qPCR) for the detection and quantification of STH infections in three drug efficacy trials in Ethiopia, Lao PDR, and Tanzania. Furthermore, we evaluated a selection of minimal diagnostic criteria of the TPPs. Principal findings All diagnostic methods showed a clinical sensitivity of ≥90% for all STH infections of moderate-to-heavy intensities. For infections of very low intensity, only qPCR resulted in a sensitivity that was superior to a single Kato-Katz for all STHs. Compared to the reference method, both Mini-FLOTAC and FECPAKG2 resulted in significantly lower fecal egg counts for some STHs, leading to a substantial underestimation of the infection intensity. For qPCR, there was a positive significant correlation between the egg counts of a single Kato-Katz and the DNA concentration. Conclusions/Significance Our results indicate that the diagnostic performance of a single Kato-Katz is underestimated by the community and that diagnostic specific thresholds to classify intensity of infection are warranted for Mini-FLOTAC, FECPAKG2 and qPCR. When we strictly apply the TPPs, Kato-Katz is the only microscopy-based method that meets the minimal diagnostic criteria for application in the planning, monitoring and evaluation phase of an STH program. qPCR is the only method that could be considered in the phase that aims to seek confirmation for cessation of program. Trial registration ClinicalTrials.gov NCT03465488, Author summary To control the burden caused by intestinal worms, the World Health Organization recommends large-scale deworming programs where anti-worm drugs are administered to at-risk populations. The decision to scale down drug distribution is based on the periodically assessment of prevalence and intensity of infections using a standard diagnostic method. Today, the scientific community strongly doubts whether this method can be used throughout the program. This is in particular when it fails to detect infections of low intensity, and hence may result in prematurely stopping the distribution of drugs. We compared the diagnostic performance of alternative diagnostic methods in three drug efficacy trials in two African and one Asian country. The diagnostic methods were based on demonstration of worm eggs or worm DNA in stool. We also checked the results with minimal diagnostic criteria which have been recently been proposed by the scientific community. Our results indicate that of all diagnostic methods based on demonstration of worm eggs, only the current standard method fulfills the diagnostic criteria for planning, monitoring and evaluation phases of deworming program. Furthermore, we showed that DNA-based methods could be considered in the phase that aims to seek confirmation for cessation of the deworming program.