Mycobacterium avium subspecies paratuberculosis (Map) is the known cause of Johne's disease of ruminants and has been implicated as a cause of Crohn's disease in humans. Previous work has shown that Map is present in untreated water entering water treatment works (WTWs) in Northern Ireland. The work reported here was directed at extending this study by developing both molecular and culture methods for detecting Map and using them to conduct a limited survey of two local WTWs. These have the same source water, Lough Neagh, but have different water treatment systems viz. WTW1 is based primarily on slow sand filtration (SSF) while WTW2 is based on dissolved air floatation (DAF). The SSF process incorporates a schmutzdecke which is a biologically active 'dirty layer' responsible for most of the bactericidal effects while DAF causes particulate matter, including microorganisms, to flocculate and rise to the surface where they are physically removed. This work not only allowed the efficiency of the water treatment processes to kill or remove Map to be determined but also compare the two respective water treatment systems. The survey was carried out over a 9-month period to take account of seasonal effects and husbandry practices. The molecular method used was based on centrifugation, filtration and in-house immunomagnetic separation (IMS) followed by conventional and real-time PCR, the latter based principally on the IS900 insertion element. The method was calculated to have a sensitivity of 10 Map cells ml^-1. Map was found throughout both WTW processes from source water to final treated water. No definite concentration of the organism was found at any particular stage. It is recognized that the PCR method employed does not distinguish between viable and non-viable cells. It is hoped that the culture methods that have been performed in parallel with these PCR assays will shed light on this question. It is also hoped that laboratory biofilm studies will provide more fundamental information on the behaviour of Map during both water treatment processes. Since water is one of the possible routes of transmission, the outcome of this work should contribute to a more meaningful risk assessment of the public's exposure to Map and hence inform on possible intervention strategies.