The present study examined effects of Azorubine (E122) and Amaranth (123) on male reproductive system of Swiss albino mice. Control (Group I, n=20) was treated with vehicle. Two treatment groups based on azorubine (Group II) and amaranth (Group III) treatment were designed with sub-groups for doses 1/2LD50 and 1/4LD50 (Group IIa, Group IIb, Group IIIa and Group IIIb) consisting of 20 animals each. Five animals from each group and sub-group were sacrificed at 7th, 14th, 21st, and 28th day of administration. Body and testis weight were measured, along with cauda sperm characteristics and testicular histology. Level of reproductive hormones were also examined. Results showed significant deterioration of sperm characteristics after treatment with both dyes. Major types of sperm deformities noticed in azorubine and amaranth treated animals were broken tail, bend tail, cytoplasmic droplet, head-tail separation, coiled tail, and headless sperms. More than 30% decline in motility and abnormality was noted in animals treated with amaranth. Histological observation indicated cytotoxic damages in amaranth treated mice, while azorubine treated animals exhibited large scale disorganization of germ cells and interference in spermatogenesis. Conclusively, azorubine and amaranth at the doses used in this study were detrimental to spermatogenesis. Deformities found in the cauda epididymal sperms indicated consequential impact on the rate of fertility.