Integrated livestock-fish aquaculture utilizes animal excreta and urine as pond fertilizers to enhance growth of plankton and other microorganisms eaten by the fish. In Vietnam, pigs are commonly integrated with fish and horticulture in household-based VAC systems (vuon = garden; ao = pond; chuong = pigsty), but the level of fecal contamination in the fish produced is unknown. This study was carried out to assess the level Escherichia coli contamination of fish meat and gut contents of grass carp (Ctenopharyngodon idellus), silver carp (Hypophthalmichthys molitrix), and rohu (Labeo rohita) cultured in randomly selected five VAC ponds (with pig manure) and five non-VAC ponds (without pig manure) at sites in periurban Hanoi, Vietnam. Fish muscle tissue samples contained E. coli at <10 or 320 or 820 CFU/g, regardless of the culture system from which they originated. In contrast, the intestinal contents of fish raised in manure-fed ponds contained E. coli at 4.75, 5.25, and 5.07 log CFU/g for silver carp, grass carp, and rohu, respectively, about 100 times higher than the contamination of fish from the control ponds. The results indicate that muscle tissue of fish raised in VAC systems has a low level of fecal contamination despite high levels of E. coli in their gut. Thus, a critical point to control food safety of such fish is the prevention of fecal cross-contamination during degutting and cleaning of the fish at markets and in the home.