This study was done to assess the risk of helminth infection in association with wastewater-fed rice cultivation in an agricultural setting of Nam Dinh city, Vietnam. In a cross sectional survey data were collected for 202 households in a commune where wastewater was used for irrigation and for 201 households in a commune that used river water. Parasitological examination was conducted on single stool samples obtained from 1,088 individuals aged ≥15 years from the households. The irrigation water used in both communes was enumerated for helminth eggs and thermotolerant coliforms. The prevalence of infection with Ascaris spp., Trichuris spp., and hookworm was 42.2%, 19.9% and 10.5% respectively, with an overall prevalence of infection with any helminth of 53.4%. Surprisingly, the prevalence of infection with Ascaris and Trichuris was lower among people exposed to wastewater (containing 40–200 helminth eggs/l and 104 thermotolerant coliforms/100 ml) compared to people exposed to river water that contained lower worm egg and bacterial numbers. Poor sanitation and hygiene practices and not using protective measures were important independent risk factors for helminth infection. For hookworm infection, no significant difference was observed between the wastewater exposed and unexposed groups. Children living in the wastewater use area had a significantly better nutritional status than those in the area using river water. This suggests a generally higher welfare level of the wastewater use area. In conclusion, this study showed no evidence that rice cultivation with wastewater poses a risk for helminth infection. More detailed studies are needed on the reduction of fecal indicators and helminth eggs in peri-urban wastewater-irrigated rice culture systems and on the relative importance of wastewater irrigation compared to other risk factors for human helminth infection such as poor sanitation and poverty.