Background E.coli O157 is a bacterial pathogen that is shed by cattle and can cause severe disease in humans. Phage type (PT) 21/28 is a subtype of E.coli O157 that is found across Scotland and is associated with particularly severe human morbidity. Methods A cross-sectional survey of Scottish cattle farms was conducted in the period Feb 2002-Feb 2004 to determine the prevalence of E.coli O157. Data from 88 farms on which E.coli O157 was present were analysed using generalised linear mixed models to identify risk factors for the presence of PT 21/28 specifically. Results The analysis identified private water supply, and northerly farm location as risk factors for PT 21/28 presence. There was a significant association between the presence of PT 21/28 and an increased number of E.coli O157 positive pat samples from a farm, and PT 21/28 was significantly associated with larger total E.coli counts than non-PT 21/28 E.coli O157 isolates. Conclusions There are significant differences in the risk factors for the presence of different phage types of E.coli O157. This finding has implications for the control of E.coli O157 as a whole and suggests that control could be tailored to target the locally dominant PT.