Extensive literature suggests that melatonin play a role against the degenerative effect of central neurotoxins by its acting as free radical scavenger. This study aimed at evaluation of the anti-mutagenic activity of novel synthesized indole derivatives 2, 4a, and 8 in albino male mice in comparison with the parent melatonin. Efficacy of melatonin and its derivatives to influence cyclophosphamide (CP)-induced genotoxicity was tested using micronuclei (MN) formation in the bone marrow cells and determination of DNA, RNA and protein levels as well as cholinesterase and peroxidase activities in several organs of male mice. Following intragastrical injection of melatonin or one of its derivatives daily for 1 week, CP was given intraperitoneally, i.p., as a single dose of 25mg/kg BW. Pyridazin-4-yl thiadiazoloindole derivative 8, diaminothiophen-5-yl thiadiazoloindole derivative 4a and melatonin were significantly able to reduce the number of micronucleated polychromatic erythrocytes (MnPCEs) in the bone marrow cells induced by CP (P<0.0001, P<0.001, P<0.01, respectively). However, reduction of MN formation in the bone marrow cells was not significant when thiadiazoloindole derivative 2 was administered (P=0.14). Examination of the protective effect of melatonin and its derivatives on the levels of DNA, RNA and protein as well as enzyme activities showed that compound 8 had the ability to inhibit the clastogenic effect of CP in several organs of male mice. These findings suggest that compounds 4a, 8 and melatonin were able to reduce the mutagenicity effect of CP in male mice. The ability of compounds 4a, 8 and melatonin to reduce CP-related genotoxicity is possibly attributed to their antioxidant activity.