Schistosomiasis is a neglected tropical disease (NTD) caused by blood flukes from the genus Schistosoma. Brazil hosts the main endemic area in the Americas, where Schistosoma mansoni is the only species causing the disease. Kato-Katz (KK) thick smear is the WHO recommended screening test for populational studies, but there is growing evidence for the sensitivity limitations associated with KK, especially in areas with low parasite loads. Helmintex (HTX) is another highly sensitive egg-detection method, based on the magnetic properties of S. mansoni eggs and their isolation in a magnetic field. The objective of this study is to evaluate both KK and HTX in a moderate endemic locality, Areia Branca, located in the municipality of Pacatuba, in the state of Sergipe in northeastern Brazil. From 234 individual fecal samples, two KK thick smears were prepared and evaluated for each sample. Similarly, 30 g of each fecal sample was processed by HTX protocol. Eggs were detected in 80 (34.18%) residents. Twenty-three (9.83%) samples were positive for eggs (only by KK), and 77 (32.91%) samples showed positive for eggs (only by HTX). Sensitivity, specificity, and accuracy estimates gave values of 28.75%, 100% and 75.64%, respectively, for KK, and 96.25%, 100% and 98.72% respectively, for HTX. The positive predictive value was 100% for both methods, while the negative predictive value was 72.99% for KK and 98.09% for HTX. Overall, HTX presented a superior performance compared to the one sample, two slides KK examination. The study confirms the role of HTX as a reference method for the definition of true-positive samples in comparative accuracy studies and its potential role in the late stages when the certification of schistosomiasis transmission interruption is required. Diagnostic tests are important tools for the elimination of this NTD, besides the effective implementation of safe water, basic sanitation, snail control, and the treatment of infected populations.