This study was aimed to compare the effects of different adjuvants on male reproductive function in rats immunized using GnRH2-MAP. Male Sprague-Dawley rats were assigned to control, ISA 201 adjuvant and Gel 01 adjuvant groups along with GnRH2-MAP. The serum testosterone and antibody titers were measured every 2-week by ELISA, the testes were weighed and histologically analyzed. mRNA expression levels in the hypothalamus, pituitary, and testes were determined by RT-qPCR. Among the three groups, the ISA 201 adjuvant group exhibited the lowest testosterone concentration (P<0.05), the highest antibody titer (P<0.05), and testis atrophy. GnRH mRNA expression in the hypothalamus; GnRH-R, FSH-β, and LH-β expression in the pituitary; and FSH-R, LH-R, and 3β-HSD expression in the testes were significantly lower in this group (P<0.01). Additionally, several other genes showed significant differential expression in the ISA 201 adjuvant group than in the other two groups. It is concluded that the GnRH2-MAP vaccine emulsified with ISA 201 adjuvant is more effective than that administered with Gel 01 adjuvant. , 2019. Effect of active immunization using gonadotropin-releasing hormone 2-multiple antigen peptide with different adjuvants on the reproductive functions of male rats. Pak Vet J, 39(2): 205-210. http://dx.