Leptospirosis is a common global zoonotic disease of man and all farm animals. Although most leptospiral infections in sheep and goats are asymptomatic, they may play a role in the epidemiology of the disease by the spread of Leptospira through the urine. This study was carried out to evaluate the role of sheep and goats in the epidemiology of leptospirosis. Blood and urine samples were taken from 210 goats and 246 sheep. To detect antibodies, sera samples were tested with 8 live serovars of L. interrogans (Hardjo, Pomona, Grippotyphosa, Canicola, Ballum, Icterhemorrhagiae, Tarasovi, and Australis) by MAT. Then, urine samples were tested by Nested PCR targeting 16S rRNA gene for detection of pathogenic Leptospira. Results of MAT showed that 10.95% of goats and 8.53% of sheep had antibodies against at least one examined serovars. In both species, the highest reacting was L. i. Pomona with a rate of 68.18% and 56% in sheep and goats, respectively. Moreover, in PCR, 2 (0.95%) urine samples of goat and 12 (4.87%) urine samples of sheep were positive. All of the MAT positive studied animals were PCR negative and, statistical analysis showed that there was no relationship and agreement between the results of PCR and MAT in sheep (kappa = − 0.07, p > 0.05) and goats (kappa = − 0.02, p > 0.05). Finally, it is concluded that sheep and goats can excrete L. interrogans in the urine and thus transmit them to other animals and humans.