Background: Since the emergence of COVID-19 and the pandemic declaration, this disease has become the top priority for global healthcare systems. The standard diagnostic tool for COVID-19 involves conducting imaging studies alongside real-time polymerase chain reaction (RT-PCR) tests on nasopharyngeal or oropharyngeal samples. Objectives: Given the potential extrapulmonary involvement of COVID-19, our objective was to evaluate the diagnostic effectiveness of double pharyngeal sampling, as well as the use of saliva and anal swabs. Methods: This cross-sectional study involved 102 pediatric patients suspected of having COVID-19. After the routine nasopharyngeal sampling, additional samples were collected from the nasopharynx, saliva, and anal canal. These samples were subjected to RT-PCR testing using Taq Man's probe-based technology. The statistical analysis included sensitivity, specificity, positive and negative predictive values, and Kappa agreement measurement. Results: In this study, with a COVID-19 prevalence of 92. 2%, we compared the diagnostic efficacy of different methods. When having at least one positive sample was considered the gold standard, double nasopharyngeal sampling exhibited the highest sensitivity, followed by RT-PCR of saliva and anal swabs (94. 9%, 92. 9%, and 91. 9%, respectively). When double sampling was considered the gold standard for diagnosis, saliva RT-PCR showed the highest sensitivity and negative predictive value (93. 6% and 40. 0%, respectively). However, there was no significant difference in the specificity and positive predictive value between anal swabs and saliva RT-PCR. However, when anal swabs and saliva were compared with only one nasopharyngeal sample, anal swabs performed slightly better than saliva. Conclusions: While the combination of double sampling from the nasopharynx and oropharynx, along with anal swabs and saliva, proved effective for diagnosing COVID-19, routine use of these methods may not be cost-effective. However, during periods of epidemic control, when comprehensive case identification is crucial, these methods may warrant consideration for more extensive investigations.