Cryptosporidium spp. and Giardia lamblia (synonyms: Giardia duodenalis, Giardia intestinalis) are emerging protozoa causing disease in humans and animals worldwide. These parasites can pose a serious threat to immunocompromised people, for whom the symptoms are more severe and may include abdominal pain, watery diarrhoea, nausea, headaches, malaise, and fever. One of the sources of these parasites can be treated wastewater from wastewater treatment plants (WTPs). Samples of treated wastewater (effluent), each of 10 L volume, were collected from 13 municipal WTPs located in eastern Poland. Cryptosporidium oocysts and Giardia cysts were separated by the immunomagnetic method. The presence and/or concentration of protozoan (oo)cysts in effluent samples were determined by direct immunofluorescent microscopy, nested PCR and Real Time PCR. Viability of (oo)cysts was determined by double-staining with the use of Live/Dead BacLight kit (Invitrogen). Cryptosporidium spp. oocysts were detected in 8 WTPs (61.5%) and Giardia spp. cysts in 11 WTPs (84.6%) by microscopic analysis. Both pathogens were detected in samples from 7 WTPs. Median concentrations of Cryptosporidium and Giardia (oo)cysts in 13 examined samples were 2.2/L and 6.6/L, respectively, while mean concentrations were 28.5/L and 113.6/L, respectively. In positive samples, Cryptosporidium oocysts concentrations ranged from 0.4 - 154.1 oocysts per litre, and Giardia cysts concentrations ranged from 0.7 - 660 cysts per litre. By nested PCR, Giardia DNA was detected in 4 samples of the 13 examined, (30.8%) while Cryptosporidium DNA was never detected. In Real Time PCR, positive results for Giardia were obtained in 5 samples (38.5%) and in none of the samples for Cryptosporidium, with the exception of one equivocal result. Viable (oo)cysts of Cryptosporidium and Giardia were detected in 3 out of 4 samples examined, in the ranges of 12.5 - 60% and 50 - 100% of total (oo)cysts, respectively. In view of our preliminary study, the presence of oocysts and cysts (largely viable) in effluents from WTPs imply a risk of transmission of waterborne protozoan parasites to humans. Therefore, additional wastewater purification procedures are necessary.