We report the outcome of an 11-year programme monitoring sewage water and acute flaccid paralysis (AFP) cases as part of the World Health Organization (WHO) strategy for polio eradication in the Slovak Republic (SR). Polioviruses (PV) and non-polio enteroviruses (NPEV), prior to and after the change in polio vaccination strategy, were detected. Sewage treatment plant samples from 48 localities spread over the Western, Central and Eastern regions and clinical material from AFP cases were examined. The WHO standard procedures were followed with regard to virus isolation and identification. There were 538 commonly detected human enteroviruses (HEVs) including 213 (40%) coxsackie B viruses (CBV), 200 (37%) echoviruses and 113 (21%) Sabin-like PVs (PV1, 2, 3) including vaccine-derived poliovirus (VDPV) isolates. The percentage of PV isolates fell from 66% to 30% during 2001-2005 and thereafter fell to zero. CBV5, CBV2 and echovirus 3 were the NPEVs endemic during the study period.