Background and Objectives: Cutaneous leishmaniasis is responsible for chronic and disfguring skin lesions resulting in morbidity and social stigma. The gold standard to diagnose cutaneous leishmaniasis is microscopy but has a variable sensitivity and requires trained personnel. Using four scenarios, the objective of this study is to compare the cost efectiveness of microscopy with two new tools: Loopamp™ Leishmania Detection Kit (LAMP) and CL Detect™ Rapid Test (RDT). Methods: Data related to the cost and accuracy of these tools were collected at the clinic of the National Malaria and Leishmaniasis Control Program in Kabul, Afghanistan. The efectiveness estimates were measured based on the tools’ performance but also indirectly, using the disability-adjusted life years. A decision tree was designed in TreeAge Healthcare Pro 2016, combined with a Markov model representing the natural history of cutaneous leishmaniasis. In addition to a deterministic analysis, univariate sensitivity and probabilistic analyses were performed to test the robustness of the results. Results: If the tools are compared at the National Malaria and Leishmaniasis Control Program level in a period of low incidence, microscopy remains the preferred option. LAMP becomes more appropriate during cutaneous leishmaniasis seasons or outbreaks when its capacity to process several tests (e.g. up to 48) at a time can be maximised. RDT has a cost similar to microscopy when used at the reference clinic but as it is relatively easy to use, it could be implemented at the peripheral level, which would become cheaper than employing microscopy at the reference clinic. Moreover, combining RDT with microscopy or LAMP at the reference clinic for the negative suspects is economically more interesting than directly performing LAMP or microscopy respectively on all cutaneous leishmaniasis suspects at the reference clinic. Conclusions: When taking advantage of their respective strengths, LAMP and RDT can prove to be cost-efective alternatives to using microscopy alone at the reference clinic.