Ecto-nucleotide pyrophosphatase-1 (NPP1) hydrolyzes phosphodiester bonds of ATP resulting mainly in the formation of AMP and pyrophosphate (PPi). NPP1’s activity plays a deleterious function in osteoarthritis (OA)/calcium pyrophosphate deposition (CPPD) disease. Hence, inhibitors of NPP1 represent a medical need. We synthesized ATP-α-thio-β,γ-CH2 (1), ATP-α-thio-β,γ-CCl2 (2), ATP-α-CH2-γ-thio (3) and established their resistance to hydrolysis by NPP1,-3 and NTPDase1,-2,-3 and -8 (<5% hydrolysis). Analogues 1-3 at 100 mM inhibited NPP1 and NPP3 by > 90% and 23-43%, respectively, and only slightly affected (0-40%) hydrolysis of ATP by NTPDase1,-2,-3,-8. Analogue 3 is a potent NPP1 inhibitor, Ki 20 nM. Analogue 2a is a selective NPP1 inhibitor, Ki 685 nM. Analogues 1-3 were mostly non-agonists of P2Y1/P2Y2/P2Y11 receptors. We next developed NPP1 inhibitors based on uridine 5’-Pα,α-di-thiophosphate analogues, 4-7, to maintain the favorable pharmacological properties of 1 and 2, while avoiding a chiral center at Pα-phosphate, and the waste of half of the nucleotide. Analogues 4-7 proved to be stable to air-oxidation and to acidic and basic pH. All analogues potently inhibited hNPP1 (80-100% inhibition) at 100 µM, with no inhibition of the related NPP3 and ectonucleotidases (NTPDase1,2,3,8). Likewise, these compounds showed nearly no activity at P2Y2,4,6-receptors. A promising analogue was diuridine-5`,5”-O-Pα,α–tetrathiotetraphosphate, 7, Ki 27 nM. Docking simulations have indicated that the origin of enhanced NPP1 inhibitory activity and selectivity of 7 is the simultaneous occupancy of both binding-sites of the NPP1 by 7. NPP1 inhibitor, 2, was not toxic to chondrocytes and was stable in culture medium and human plasma. 2 effectively inhibited NPP1 activity in whole human cartilage and in chondrocytes and reduced extracellular PPi accumulation. Therefore, we suggest potent and selective inhibitors of NPP1 for lowering extracellular PPi levels in cartilage for preventing and treating OA/CPPD.