Colonoscopy is a well recognized diagnostic and therapeutic tool. Endoscope reprocessing must be done correctly every time; a breach of protocol leading to transmission of infection has the potential to bring endoscopy to a halt. Standards exist that guide the practitioner in all health care settings to minimize the chance of transmission of infection. Safe injection practices and reprocessing of endoscopes using high-level disinfection and sterilization methods may help avert the risk of contracting possible infections during colonoscopy procedures.