BACKGROUND: Cutaneous Leishmaniasis (CL) is underreported in Sub-Saharan Africa. Only a few studies reported the use of molecular diagnostic methods for CL in the region, whereas reports of therapeutic outcomes are scarce. METHODS: An international consortium was established between local teams in the Zinder region of Niger and a referral centre for leishmaniasis in French Guiana. Specific training on CL diagnostic was provided by the Guianese team to Nigerien health workers. All consenting patients with clinically suspected CL lesions were enrolled. Samples were made for parasitological smear and PCR on cotton swabs. Then, participants were treated as per local protocol with oral metronidazole for 14 days and were followed for 4 months. RESULTS: In total, 59 clinically suspected CL cases were included, among whom 33 (56%) were confirmed by PCR and/or by microscopy, including 21 men and 22 women, 23 minors and 10 adults. 32 (97%) of them presented with ulcers (including 12 with ulcers and nodules). The median number of lesions was 2 [IQR 1-3]. The most frequent location of lesions was the lower limbs (21/33, 63.6%), followed by the upper limbs (14/33, 42.4%). One mucosal involvement was reported but unconfirmed with PCR. The efficacy of oral metronidazole was 90.9% (30/33) among confirmed cases and 76.3% (45/59) in the overall study population. The documented species was Leishmania major. CONCLUSIONS: This is the first report of PCR-proven human CL in Niger, and the first report of a human CL case in the Zinder area for more than a century. Molecular techniques confirmed the circulation of L. major in this area, which until now had only been determined by isoenzymes analysis. Presenting CL patients were very young. Treatment outcomes with metronidazole were encouraging. This prompts for a formal evaluation of the efficacy of this drug, ideally in a randomized controlled trial.