Shiga-toxigenic Escherichia coli (STEC) O157 and several serogroups of non-O157 STEC are frequently identified as the causative agents of large outbreaks and sporadic cases of hemorrhagic colitis as well as hemolytic uremic syndrome, a life threatening sequelae. Ruminants are considered an important reservoir of STEC. In Malaysia, the data on prevalence of STEC serotypes in ruminants is limited. A total of 136 ruminant faeces which included cattle, buffalo, sheep and goat faeces were collected from 6 different ruminant farms in Malaysia to isolate STEC. Multiplex PCR was used to screen samples for the presence of STEC using the target virulence genes for Shiga toxin 1 and 2 (stx1 and stx2), attaching and effacing factor (eaeA) and enterohemolysin (ehxA), while immunomagnetic separation was used to isolate STEC serogroup O157. STEC O157:H7 was isolated from 4% of faeces (all samples from a single farm) and all 32 isolates obtained carried stx2, eaeA and ehxA. STEC non-O157 was isolated from 19.2% of faeces (samples from four different farms) with most isolates (26 out of 48, 54.2%) carrying both stx1 and stx2, 14.6% carrying stx1 and 29.2% carrying stx2. Both eaeA and the ehxA were present in 47.9% of the STEC non-O157 isolates. The presence of STEC O157 and non-O157 in ruminant faeces suggests that the ruminants in Malaysia are a reservoir of STEC and may be a source of STEC entry into human food chain. Further characterisation of the isolated STEC O157 and non-O157 serogroups could provide a better understanding of the diversity of STEC in Malaysia and their pathogenic potential.