History of surgical wounds drainage is long-lasting. In our research we focused on the debated issue of safety and effectiveness of drainage. In the period 2006–2008 we were examined 198 samples of patients after arthroplasty, or one-stage exchange for aseptic loosening and and 202 patients with infected artrhoplasty. For all patients was performed a prospective study of drain contamination using PCR methods. Research has confirmed that the Redon drainage is a safe method that provides a clear benefit for the pacient. Based on the results of this study is recommended to keep drains 2 days after surgery. Negative factor for the colonization of the drain are higher postoperative blood loss. Continuous irrigation drainage can be clearly classified into standard operating procedures in the treatment of infectious diseases in the orthopedic. The use of irrigation drainage brings benefit over risk. Prolonged irrigation drainage did not remove the contamination from the drains. Handling with irrigation drainage systems and dressing exchange did not a risk factor of contamination. For infected knee joint is recommended to leave irrigation drainage about 100–112 hours, follow sucktional drainage and further 12 to 24 hours to remove the drains. An important finding is the frequent presence of pathogenic fungi in the DNA material from arthroplasty area.