Introduction Both obesity and diabetes play a significant role in reproductive disorders in women and insulin resistance (IR) is a confirmed trait d’union. We evaluated the relationship between IR and an established ovarian reserve biomarker such as anti-mullerian hormone (AMH) together with other potential modulators of ovarian physiology (adiponectin and kisspeptin) in young reproductive-aged group women with obesity and type 1 diabetes (T1D). Patients and methods We recruited 32 female youths: 14 of them presented with T1D (14.6 ± 2.6 years) and 18 with obesity (15.1 ± 2.6 years). The control group included 20 age-matched normal weight females. Each patient underwent physical examination and hormonal assessment. AMH, kisspeptin and adiponectin levels were also measured. IR was calculated as the homeostasis model assessment for insulin resistance (HOMA-IR) and the glucose disposal rate (eGDR) in patients with obesity and with T1D, respectively. Results adiponectin and kisspeptin levels were significantly different into groups (p ≤ .001), whereas AMH levels were not. Adiponectin values were higher in controls compared to patients with obesity (p < .001) and T1D (p = .02). Kisspeptin levels were lower in controls compared to patients with obesity (p = .001), without reaching statistical significance when compared to T1D (p = .06). IR was associated with lower adiponectin and higher kisspeptin levels (p < .001 and p = .02, respectively), but not with AMH. Conclusions IR displays a relationship with adiponectin and kisspeptin in young reproductive-aged women with obesity and T1D. Interventions to correct IR in adolescents could be part of an early approach to prevent reproductive disorders and to promote factors associated with longevity in adult women.