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Background Soil-transmitted helminths and intestinal protozoa infection are widespread in developing countries, yet an accurate diagnosis is rarely performed. The aim of this study was to evaluate the recently developed mini–FLOTAC method and to compare with currently more widely used techniques for the diagnosis of intestinal parasitic infections in different settings. Methodology/Principal Findings The study was carried out in Dharamsala, Himachal Pradesh, India, and in Bukumbi, Tanzania. A total of 180 pupils from two primary schools had their stool analyzed (n = 80 in Dharamsala and n = 100 in Bukumbi) for intestinal parasitic infections with three diagnostic methods: direct fecal smear, formol-ether concentration method (FECM) and mini-FLOTAC. Overall, 72% of the pupils were positive for any intestinal parasitic infection, 24% carried dual infections and 11% three infections or more. The most frequently encountered intestinal parasites were Entamoeba coli, Entamoeba histolytica/dispar, Giardia intestinalis, hookworm, (and Schistosoma mansoni, in Tanzania). Statistically significant differences were found in the detection of parasitic infections among the three methods: mini-FLOTAC was the most sensitive method for helminth infections (90% mini-FLOTAC, 60% FECM, and 30% direct fecal smear), whereas FECM was most sensitive for intestinal protozoa infections (88% FECM, 70% direct fecal smear, and 68% mini-FLOTAC). Conclusion/Significance We present the first experiences with the mini-FLOTAC for the diagnosis of intestinal helminths and protozoa. Our results suggest that it is a valid, sensitive and potentially low-cost alternative technique that could be used in resource-limited settings — particularly for helminth diagnosis., Author Summary The mini-FLOTAC has been recently developed as a novel direct method for the diagnosis of intestinal parasitic infections. Mini-FLOTAC attempts to address the challenge of using modern technology matched with high sensitivity, affordability, and appropriateness of diagnosis in resource-limited settings where intestinal parasitic infections are widespread. We compared accuracy and feasibility of mini-FLOTAC with currently more widely used diagnostic methods, such as the direct fecal smear and the formol-ether concentration method. Our study was carried out in Dharamsala, India, and in Bukumbi, Tanzania in order to evaluate the methods under different field conditions and diverse parasitic infection profiles. Among 180 primary schoolchildren examined, 72% were positive for any intestinal parasitic infection. Mini-FLOTAC detected the highest number of helminth infections (90% sensitivity), whereas the formol-ether concentration was the most sensitive approach for intestinal protozoa infections (88% sensitivity). The logistic advantages of mini-FLOTAC are that the procedure does not require any centrifugation step or expensive equipment, it can be performed on fresh and fixed stool samples, and only requires 10–12 min of preparation before microscopic analysis. Our data suggest that mini-FLOTAC is a promising diagnostic tool for helminth diagnosis; therefore, follow-up studies in other settings are warranted.