This paper describes the application of two direct and one indirect methods for the extraction of microbial community DNA from soils polluted with heavy metals. DNA was extracted directly from soil by a gentle method based on the soil incubation at 37°C with proteinase K and SDS or the method was modified by the addition of bead beating step. The indirect approach was based on the RNA/DNA extraction method. The level of soil contamination did not affect on the yields of DNA extracted and PCR amplification of the target DNA. The results indicated that the DNA obtained by the applied protocols was sufficiently pure for further molecular analyses.