Human cytomegalovirus (HCMV) is the most frequent cause of congenital infection. Diagnosis of this infection is important because 5-17% of asymptomatic infected babies will develop late sequelae and should be followed closely. Most of these children will remain undetected, since screening of all newborns by viral Culture is too expensive. The aim of this study was to demonstrate that pool testing could be used to detect HCMV congenital infection in newborns. For this purpose, a nested-PCR technique was tested in urine pools. In phase 1, urine specimens were tested alone by nested-PCR and compared with viral culture, followed by cross experiments to test the reliability of detecting one positive specimen in a 20 samples in a urine pool. In phase 2, this pool method was applied to all urine specimens from children received in the virology laboratory of the Centro Hospitalar Cova da Beira for diagnosis of HCMV infection, between January 2002 and March 2003. In phase 1, 74 urine specimens were tested simultaneously by shell-vial culture and nested-PCR; 17 were positive and the remaining 57 negative by both methods. The negative specimens were divided into three pools and each pool was tested alone and crossed with each of the positive specimens by nested-PCR. Although the three pools were negative when tested alone, all 51 crossed results were positive. In phase 2, 15 out of the 180 urine samples tested positive by shell-vial culture and were detected by this pool method. These results suggest that urine pools can be used to detect HCMV positive urines in children, with similar sensitivity and specificity when compared with the standard method, but with a substantial labour reduction. This significant reduction in labour and consequently in cost per test, opens the possibility of applying PCR to urine pools for screening the HCMV congenital infection in newborns.