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Soil-transmitted helminths (STH) including the hookworms Necator americanus and Ancylostoma spp., Ascaris lumbricoides, and Trichuris trichiura affect over 1.5 billion people worldwide and are estimated to have caused 1.9 million disability-adjusted life years (DALYs). With the concerted effort in expanding and improving targeted mass drug administration (MDA) programs over the past decade, along with decreasing prevalence, infections in several endemic areas tend to be of low intensity. Conventional microscopy-based methods recommended for the detection of STH in parasitological surveys have been shown to be less sensitive in these low-intensity settings. As communities progress towards STH elimination through MDA and improved sanitation, there is a pressing need for highly sensitive techniques that detect the true prevalence of STH to evaluate the effectiveness of ongoing programs and interventions. Molecular methods that involve analysis of DNA rather than the morphology of the organism are highly sensitive and specific, allowing for both quantitation and species discrimination. The following review discusses different sample collection strategies, pre-processing steps, DNA extraction platforms, and nucleic acid detection methods available for diagnosis and surveillance of STH. We have contrasted the utility of these molecular tools against conventional microscopy-based methods currently used in most endemic settings. While the detection methods are primarily qPCR based, several newer technologies have also become available along with automation and increased throughput, making these molecular tools increasingly cost-effective and potentially amenable for use in low-resource settings.