Ketosis‐prone diabetes (KPD) is a phenotypically defined form of diabetes characterized by male predominance and severe insulin deficiency. Neurogenin3 (NGN3) is a proendocrine gene, which is essential for the fate of pancreatic β cells. Mice lacking ngn3 develop early insulin‐deficient diabetes. Thus, we hypothesized that gender and variants in NGN3 could predispose to KPD. We have studied clinical and metabolic parameters according to gender in patients with KPD (n = 152) and common type 2 diabetes (T2DM) (n = 167). We have sequenced NGN3 in KPD patients and screened gene variants in T2DM and controls (n = 232). In KPD, male gender was associated with a more pronounced decrease in β‐cell insulin secretory reserve, assessed by fasting C–peptide [mean (ng/ml) ± s.d., M: 1.1 ± 0.6, F: 1.5 ± 0.9; p = 0.02] and glucagon‐stimulated C–peptide [mean (ng/ml) ± s.d., M: 2.2 ± 1.1, F: 3.1 ± 1.7; p = 0.03]. The rare affected females were in an anovulatory state. We found two new variants in the promoter [−3812T/C (af: 2%) and −3642T/C (af: 1%)], two new coding variants [S171T (af: 1%) and A185S (af: 1%)] and the variant already described [S199F (af: 69%)]. These variants were not associated with diabetes. Clinical investigation revealed an association between 199F and hyperglycaemia assessed by glycated haemoglobin [HbA1c (%, ±s.d.) S199: 12.6 ± 1.6, S199F: 12.4 ± 1.4 and 199F: 14.1 ± 2.2; p = 0.01]. In vitro, the P171T, A185S and S199F variants did not reveal major functional alteration in the activation of NGN3 target genes. In conclusion, male gender, anovulatory state in females and NGN3 variations may influence the pathogenesis of KPD in West Africans. This has therapeutic implications for potential tailored pharmacological intervention in this population.