Rotaviruses and Adenoviruses are reported worldwide among the main agents of gastroenteritis and, consequently, the development and validation of sensitive and cost-effective methods of detection is necessary. In this study, two approaches for detection of Rotavirus A and Adenovirus in samples of human faeces were compared: the immunological kit VIKIA Rota-Adeno and the nested-polymerase chain reaction (nested-PCR for Adenovirus) and Reverse Transcriptase-PCR (RT-PCR for Rotavirus) molecular methods. From January 2006 to July 2009, 467 samples of faeces from individuals with gastroenteritis symptoms assisted at the Hospital Infant D. Pedro (Aveiro, Portugal) were analysed for Rotavirus and Adenovirus, using the VIKIA kit. From the 467 samples, 59 (12.6%) were positive for Rotavirus and 5 (1.1%) for Adenovirus. Between December 2008 to July 2009, 18 samples were analysed by both immunologic and molecular methods. From the 18 samples, 10 were positive for Rotavirus (55.5%) and 16 for Adenovirus (88.9%) when analysed by RT-PCR and nested-PCR, respectively With VIKIA kit, 11 samples were positive for Rotavirus (61.1%) and only one was positive for Adenovirus (5.5%). Sequencing of PCR products confirmed the presence of Rotavirus in 1 sample and Adenovirus in the 10 samples that were classified as negative with VIKIA Kit. The results of VIKIA kit suggest that from the both viruses studied Rotavirus are the most incident viruses in gastroenteritis, however, molecular analysis results suggest that Adenovirus could be the most responsible for the viral gastroenteritis studied.