<![CDATA[Malaria remains a major public health concern in Jayapura, Indonesia. Limited microscopy availability in primary healthcare facilities has increased reliance on rapid diagnostic tests (RDTs) for early case detection. This study aimed to evaluate the diagnostic performance of two malaria RDTs, AllCheck® and Orient Gene®, using microscopy as the reference standard. A cross-sectional study was conducted at a primary healthcare center in Jayapura in December 2025, involving 49 patients with clinical symptoms suggestive of malaria. Capillary blood samples were collected for RDT testing and preparation of thick and thin blood smears. Diagnostic accuracy was assessed by calculating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), as well as agreement analysis using Cohen’s Kappa and McNemar test. Both RDTs demonstrated comparable diagnostic performance, with sensitivities of 93.75% (95% CI: 69.77–99.84) and specificities of 100% (95% CI: 89.42–100.00). The PPV was 100% (95% CI: 78.20–100.00), and the NPV was 97.06% (95% CI: 84.67–99.93). Agreement analysis showed almost perfect concordance between each RDT and microscopy (? = 0.953; p < 0.001). No significant difference was observed between AllCheck® and Orient Gene® results based on the McNemar test (p = 1.000). No significant association was found between diagnostic outcomes and patient sex or age group (p > 0.05). The RDTs showed good performance in detecting Plasmodium falciparum and Plasmodium vivax, but reduced sensitivity for Plasmodium malariae. In conclusion, AllCheck® and Orient Gene® RDTs demonstrate strong diagnostic performance and almost perfect agreement with microscopy, supporting their suitability for malaria screening and initial diagnosis in primary healthcare settings in Jayapura. Nevertheless, microscopy remains essential for confirming non-falciparum infections and ensuring comprehensive case detection.]]>
