Abstract Post-weaning diarrhea (PWD) in pigs is a worldwide economically important disease characterized by reduced pig performance. Although relevant, recent data on prevalence of virulence genes and pathotypes in Belgium and The Netherlands are relatively scarce. The present study investigated the prevalence of fimbrial and toxin genes of E. coli using PCR in 539 PWD-affected farms in Belgium and The Netherlands. A total of 1404 samples were collected at early onset of PWD and submitted for diagnostic examination. Following standard bacteriological isolation of E. coli, PCR analysis was performed to detect genes encoding for fimbriae (F4, F5, F6, F18, F41) and toxins (LT, STa, STb, Stx2e). The prevalence of fimbriae and toxins among E. coli isolated from PWD-affected piglets was: F4 (43.1 %), F18 (39.0 %), F41 (3.8 %), F5 (1.4 %), F6 (1.2 %), STb (54.1 %), STa (49.7 %), LT (28.3 %) and Stx2e (5.0 %). Isolates carrying both fimbrial and toxin genes were detected in 50.5 % of the cases (709 out of 1404), with 94.9% classified as enterotoxigenic E. coli (ETEC). This study confirms that ETEC is frequently isolated in PWD-affected farms with F4- and F18-ETEC pathotypes involved in 34.7 and 27.8 % of the cases, respectively.