We compared two sampling methods to assess the contamination of the Vantaa river basin by Giardia cysts and Cryptosporidium oocysts: 10-1 grab samples, the common river mussel Anadonta piscinalis, were analysed for concentration of (oo)cysts from river water. The samples were collected 2-5 times in autumn 2001 from four wastewater treatment plants and four river water sites located downstream of the plants, and six times from raw water of a drinking water plant using the river as water source. The presence of Giardia and Cryptosporidium was analysed by IF microscopy and PCR. Both cysts and oocysts were detected at all sampling sites, but oocysts were more common than cysts in river water samples. In contrast, cysts were more common in A. piscinalis. Most Cryptosporidium-positive samples were of genotype 2 and Giardia were assemblage B. In river water, MPN of Escherichia coli did not correlate to the presence of (oo)cysts. In conclusion, low (oo)cyst counts were regularly identified in the Vantaa river basin which is contaminated by discharges of treated wastewater of human origin. In general, both methods to appropriate to detect (oo)cysts, but grab samples yielded more positive results. Grab sampling is also more practical and less expensive than analysis of A. piscinalis.