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<i>Neisseria meningitidis</i> is considered as an obligate human pathogen and can cause life-threatening diseases like meningitis and/or septicaemia. Occasionally, it can be recovered from infections outside the bloodstream or central nervous system, like respiratory, ocular, joint, urogenital or other unusual sites. Herein, we present two rare cases of female genital infections due to <i>N. meningitidis</i> within a two-year period (2019–2020), identified as serogroup B (MenB) and Y (MenY), respectively. Genotypic analysis for PorA, FetA and MLST revealed the following characteristics: MenB: 7-12, 14, F5-36, 1572cc and MenY: 5-1,10-1, F4-5, 23cc, respectively. Such unusual presentations should alert the clinicians and microbiologists not to exclude <i>N</i>. <i>meningitidis</i> from routine diagnosis and the need of early detection. This is the first report in Greece, and, to our knowledge, in Europe since 2005 describing meningococcal female genital infections.