Introduction: Diarrhoea is the second leading cause of death among children, and Nigeria has the continent's highest mortality with little information on the specific cause, proportion affected by Cryptosporidium and Rotavirus, and the prevalent genotypes for Rotavirus. Aim: To identify children with diarrhoea, in Abuja in the Federal Capital Territory; to estimate the proportion of children with Cryptosporidium and rotavirus diarrhoea. Study Design: One-year cross-sectional study of children under five years with acute diarrhea. Duration: The study was conducted in Abuja from June 2018 to May 2019. Methodology: Cryptosporidium and Rotavirus ELISA were done with commercially available kits. Results: Stool samples were collected from 1450 participants, of whom 1185 (81.7%) were ambulatory, 109 (7.5%) were hospitalized, and 156 (10.7%) were controls without diarrhoea. Cryptosporidium-ELISA was positive among 274 (21.1%) children with diarrhoea and 23 (1.7%) of children without diarrhoea, with August and September as peak months for infection. Rotavirus-ELISA was positive among 231 (17.8%) children with diarrhoea and 29 (2.2%) controls, with November, December, and January as peak months. Children of 12 to 17 months were most affected for both and Rotavirus (39.8%) and Cryptosporidium (37.2%). Conclusion: Cryptosporidium and Rotavirus are essential pathogens in children, especially among Rotavirus unvaccinated children in Abuja. Local and national infrastructure is inadequate for essential surveillance of diarrhoeal disease, and this will have to be improved, together with access to virological and parasitic stool testing, to monitor the planned vaccine program, especially for Rotavirus.