Giardia intestinalis is a parasite that commonly causes diarrheal disease throughout the world. An accurate and rapid diagnosis is essential to reduce the infection. Classical diagnosis of giardiasis is performed by microscopic examination of stool samples, but in recent years many DNA-based methods have been developed. In this preliminary observational study, we compared the results of the commercial BD Max enteric parasite panel (EPP) with an in-house real-time (Rt) PCR for G. intestinalis. The study population was composed of 73 samples. Of these, 27 tested positive with both techniques and 39 tested negative. Seven samples were positive with the in-house Rt PCR and negative with the BD Max EPP. The Cohen's kappa was 0.805 (95% CI 0.670–0.940). In conclusion, these preliminary results suggest that the Rt-PCR could possibly demonstrate higher sensitivity for the diagnosis of G. intestinalis than BD Max EPP, which tended to miss infection of low intensity.