This study was initiated to evaluate and compare two DNA based techniques (PCR and real-time PCR) with Direct Microscopic Examination for detection of Trypanosoma evansi. For this purpose, seventy three females' Swiss mice were divided into two groups. In group I, 21 mice were inoculated by 104 trypanosomes. In group II, 42 mice were inoculated with 102 parasites and 5 mice in each group were kept as non infected control. The pre-patent periods were followed daily by the three assays. Results showed higher sensitivities of PCR and real time PCR using both TBR1/2 and TeRoTat1.2 primer sets than direct microscopic examination in early determination of pre-patent periods as early as 24 hours post infection. Following up the course of infection by direct microscopic examination revealed three waves of parasitemia alternated with three waves of parasite disappearance from blood. The molecular techniques (PCR and real-time PCR) were able to clearly detect T. evansi in chronic stages of low parasitemia (waves of parasite disappearance) throughout the course of infection. By testing field samples, real time PCR was more reliable in detecting and quantifying very low parasitemia in clinical camels' blood samples than PCR. In conclusion, real time PCR can be considered more suitable for screening of newly introduced animals to exclude carriers and detect early infected animals for saving free herds.