The methods currently available for genotype-specific diagnosis of T. cruzi infection still present relevant limitations, especially to identify mixed infection. In the present investigation, we have evaluated the performance of Chagas-Flow ATE-IgG2a test for early and late differential diagnosis of single and dual genotype-specific T. cruzi infections. Serum samples from Swiss mice at early and late stages of T. cruzi infection were assayed in parallel batches for genotype-specific diagnosis of single (TcI, TcVI or TcII) and dual (TcI+TcVI, TcVI+TcII or TcII+TcI) infections. The intrinsic reactivity to TcI, TcVI and TcII target antigens, including amastigote (AI/AVI/AII), trypomastigote-(TI/TVI/TII) and epimastigote (EI/ EVI/EII), at specific reverse of serum dilutions (500 to 64,000), was employed to provide reliable decision-trees for ªearlyº vs ªlateº, ªsingle vs ªdualº and ªgenotype-specificº serology. The results demonstrated that selective set of attributes ªEII 500/EI 2,000/AII 500º were able to provide high-quality accuracy (81%) to segregate early and late stages of T. cruzi infection. The sets ªTI 2,000/AI 1,000/EII 1,000º and ªTI 8,000/AII 32,000º presented expressive scores to discriminate single from dual T. cruzi infections at early (85%) and late stages (84%), respectively. Moreover, the attributes ªTI 4,000/TVI 500/TII 1,000º, ªTI 16,000/EI 2,000/EII 2,000/AI 500/TVI 500º showed good performance for genotype-specific diagnosis at early stage of single (72%) and dual (80%) T. cruzi infections, respectively. In addition, the attributes ªTI 4,000/AII 1,000/EVI 1,000º, ªTI 64,000/AVI 500/AI 2,000/AII 1,000/EII 4,000º showed moderate performance for genotype-specific diagnosis at late stage of single (69%) and dual (76%) T. cruzi infections, respectively. The sets of decision-trees were assembled to construct a sequential algorithm with expressive accuracy (81%) for serological diagnosis of T. cruzi infection. These findings engender new perspectives for the application of Chagas-Flow ATE-IgG2a method for genotype-specific diagnosis in humans, with relevant contributions for epidemiological surveys as well as clinical and post-therapeutic monitoring of Chagas disease.