DNA extraction from bird feces has advanced molecular ecological studies, but has been hampered by the enzyme inhibitors remaining in the purified DNA. In this study, flow-through columns with silica membranes were used for DNA purification to remove these inhibitors of Tag DNA polymerase effectively. Here, the purification of mitochondrial and genomic DNA of sufficient quality and quantity to allow PCR amplification of the gene encoding chromo-helicase-DNA binding protein-1 (chd1), located on the avian sex chromosome, is demonstrated. This gene segment allowed sex determination of experimental birds (Cockatiel Nymphicus hollandicus) in a fast, easy, reliable, and accurate manner.