While Nasopharyngeal swab (NPS) has consistently been the suggested sample for diagnosing Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the collection process often leads to discomfort and irritation in patients, potentially lowering the likelihood of accurate detection. Hence, there is a need for an alternative diagnostic specimen. To assess the suitability of nosaphangeal, saliva, oropharyngeal swabs and time taken for the COVID-19 Antigen Rapid Diagnostic Test (Cov-2 RDT Ag) to turn positive in relation to the polymerase chain reaction (PCR) Ct value. A cross-sectional study among 301 study participants in four selected health facilities in Mbarara City. A structured questionnaire was used to collect the demographic characteristics of participants and nasopharyngeal, oropharyngeal swabs and saliva were collected. Cov-2 RDT Ag (Standard Q- South Korea) and PCR Genexert system (USA) were used in the detection of SARS-CoV-2. The time taken for RDT to turn positive and cycle threshold (Ct) values for the positive outcomes were recorded. The overall positivity rate was 06 (2.0%) by nasopharyngeal using PCR which is the gold standard. Out of the 06, saliva and oropharyngeal swabs gave 5 (83.3%) & 6 (100%) respectively using PCR. Using CoV-2 RDT Ag, the saliva, OS and NPS were 0%, 2 (33.3%), and 4 (66.7%) respectively. Samples with low Ct values took less time (mean