A series of indole conjugated bisphosphonate derivatives have been synthesized and evaluated for their in vitro anti-bone resorptive activity using bone marrow osteoclast culture. Two bisphosphonates 23 and 24 significantly inhibited osteoclastogenesis, 23 showed inhibition at 10 and 100pM which was lower than the concentration of standard drug alendronate, and 24 inhibited osteoclastogenesis at 100nM which was comparable to alendronate. Two other compounds 13 and 14 also showed inhibition comparable to alendronate, but were cytotoxic in the osteoblast cells. The two active bisphosphonates 23 and 24 induced significant osteoclast apoptosis at concentrations 100nM for compound 24 and at 10pM for compound 23 compared to alendronate. In vivo effect of active bisphosphonates 23 and 24 resulted in osteoclastogenesis of bone marrow cells (BMCs) to almost 40–50% (23 showing 8.4% decrease and 24 showing 9.0%) compared to 16.5% of the ovariectomized group. Further, screening of anti-leishmanial activity, four compounds 24–25 and 27–28 showed more than 80% inhibition against both the promastigote and amastigote stages of the Leishmania parasite.