Giardia intestinalis is a widespread parasitic protozoa which has great significance as a public health threat. Molecular diagnostics of stool sample can be unreliable because of the presence of inhibitors of enzymatic reactions. The aim of this study was to determine the effectiveness of selected pre-treatment methods of fecal samples for further PCR-based diagnostics of G. intestinalis, and the effect of each component of pre-treatment solutions on PCR reactions. Seven stool concentration techniques were compared. The results showed that the most efficient concentration method for stool sample preparation for detection of G. intestinalis by PCR is centrifugal flotation with Percoll (with saturated NaNO3 as the flotation solution). This method is relatively inexpensive, less labor-intensive, and suitable for epidemiological monitoring and clinical investigations.