During the past years surveillance for avian influenza has been conducted in the live bird markets (LBMs) in New York as well as other states along the east coast. Repeated attempts to eradicate H5 and H7 influenza from the New York markets have focused efforts on the LBMs themselves. Despite repeated mandatory market closures accompanied by cleaning and disinfecting (C/D) procedures, avian influenza virus continued to be isolated. In an effort to assess the adequacy of the C/D procedure, samples were collected in temporal proximity to the depopulation and C/D. Comparison of the pre-C/D (83% virus positive), at C/D approval (1.6% positive) and post-C/D testing (33% positive) indicate that the current procedures of C/D can be effective at eliminating these influenza viruses. However, reinfection via introduction of influenza-virus–positive birds can occur shortly after the market reopens.