Decisions on individual or community treatment and evaluation of chemotherapy based control programs depend on parasitological diagnostic techniques. The aim of this study was to compare the accuracy of a single Kato-Katz thick smear and a single FLOTAC for the determination of the prevalence and intensity of soil-transmitted helminth infections. A total of 271 faecal specimens were collected from schoolchildren in Ethiopia, and microscopically examined using the Kato-Katz method (41.7 mg stool per slide) and the FLOTAC technique. The combined results from the Kato-Katz and FLOTAC methods were used as diagnostic 'gold' standard for reference in the analysis. Agreement between the two methods showed kappa values of 0.74, 0.73 and 0.28 for Ascaris lumbricoides, Trichuris trichiura and hookworm, respectively. A single FLOTAC revealed significantly more infections than a single Kato-Katz for each of the three soil-transmitted helminths (p<0.01). The sensitivities of a single Kato-Katz for diagnosis of T. trichiura, A. lumbricoides and hookworm infections were 76.6%, 67.8% and 19.6%, respectively, while the sensitivity of FLOTAC was 100% for all the three soil-transmitted helminth species. A single Kato-Katz yielded considerably higher mean faecal egg counts (FECs) (729.1, 145.2 and 60.7 eggs per gram of stool (EPG) for A. lumbricoides, T. trichiura and hookworm, respectively) compared with a single FLOTAC (142.5, 54.5 and 14.6 EPG, respectively) (p<0.05). Our study confirms that a single FLOTAC is more sensitive than a single Kato-Katz for the diagnosis of soil-transmitted helminth infections, but results in lower FECs. Further standardization and validation are still required in different epidemiological settings with varying levels of intensity of infections before recommending FLOTAC for large-scale community diagnosis. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.