Cytokine and AMH profiling were done in prepubertal Murrah buffalo heifers post-progesterone supplementation and co-synchronization protocol. Cytokines: IFNγ, IL6, IL1, IL13, TNFα, and TGFβ, and, AMH, Progesterone and Estrogen hormone estimations were done. Ovarian follicular pattern and fertility outcome were recorded. Eighteen prepubertal heifers, 15-17 months of age, 250-300 kg BWt were randomly divided into 3 groups, Group1: n=6, supplemented with altrenogest 0.044mg/kg/day/heifer orally for 14 days along with Co-synch programme; Group2: n=6, administered CIDR for 14 days and co-synch programme, Group3: n=6, received co-synch programme. Ultrasonography was done to ovarian follicle status on respective days of sampling. Pregnancy diagnosis was done around 45 and 60 post-AI. Estradiol 17-β level remained constant in altrenogest group, CIDR implanted and Control groups during the Progesterone treatment and Co-synch treatment. Estradiol levels during Co-synch were significantly less on day 9 of Co-synch (14.41 ± 1.97 pg/mL) than day 0 and on day7 in pre pubertal buffalo heifers in altrenogest group. However, no significance was observed in other groups. Progesterone levels in buffalo heifers subjected to synchronisation protocols varied significantly (P< 0.05) on day 7 of P4 treatment between altrenogest supplemented and CIDR implanted groups, as well as, Co-synch groups. Supplementation of altrenogest showed a significant (P= 0.043) increase in Progesterone levels by day 14 of altrenogest treatment. Progesterone varied significantly in all Groups on day 9 of co synch protocol [ Group 1 (P= 0.02), Group 2 (P= 0.041) and Group 3 (P= 0.007)]. Cytokine IFN-γ showed high correlation with progesterone, indicating the role of IFN-γ in puberty in buffalo heifers (r= 0.626, P< 0.01). AMH had a significant positive correlation supplemented with altrenogest with IFN-γ (r= 0.673, P< 0.01) and TGF-β (r= 0.463, P< 0.01), whereas, with TNF-α it was a negatively correlated (r= -0.34, P< 0.05). Based on Karl Pearson correlation coefficients, IL-13 and TGF-β could be considered as markers for puberty in buffalo heifers.