A system for automated filling of syringes with medicines from containers, said syringes being of various sizes and types all having a barrel, an annular flange encircling said barrel, a plunger slidably engaged in said barrel, and a flange at distal end of said plunger, the system comprising: a bulk medicine container storage assembly for storing a plurality of bulk medicines in containers; a programmable controller programmed with control software comprising computer instructions stored on non-transitory computer memory for determining a syringe size to fill a prescription, for guided retrieval of a selected bulk medicine container to fill said prescription, for guiding retrieval of a selected syringe, and for controlling automatic filling of said syringe with medicine from said container; and a syringe storage assembly (3, 113, 114) for storing a plurality of syringes of various sizes and types; an automated filling station in data communication with said programmable controller for automatically filling said selected syringe with medicine from said selected container of medicine, a first linear conveyor in communication with said programmable controller and having a first shuttle movable therealong for automatically retrieving said selected syringe from said syringe storage (3, 113, 114) assembly under the control of said programmable controller; a syringe loading assembly for automatically moving said syringe from said first linear conveyor to a filling position at said automated filling station under the control of said programmable controller; and a second linear conveyor in communication with said programmable controller and having a second shuttle movable therealong for automatically conveying said selected bulk medicine container from said bulk medicine container storage assembly to said automated filling station under control of said programmable controller; wherein said automated filling station further comprises a plurality of arms (110, 111, 112, 128) for manipulating said syringe, said plurality of arms (110, 111, 112, 128) each terminating in a forked end for engaging the syringe, and each arm (110, 111, 112, 128) being independently controlled and articulating along two axes to withdraw a plunger of said syringe to fill said syringe with medicine. a bulk medicine container storage assembly for storing a plurality of bulk medicines in containers; a programmable controller programmed with control software comprising computer instructions stored on non-transitory computer memory for determining a syringe size to fill a prescription, for guided retrieval of a selected bulk medicine container to fill said prescription, for guiding retrieval of a selected syringe, and for controlling automatic filling of said syringe with medicine from said container; and a syringe storage assembly (3, 113, 114) for storing a plurality of syringes of various sizes and types; an automated filling station in data communication with said programmable controller for automatically filling said selected syringe with medicine from said selected container of medicine, a first linear conveyor in communication with said programmable controller and having a first shuttle movable therealong for automatically retrieving said selected syringe from said syringe storage (3, 113, 114) assembly under the control of said programmable controller; a syringe loading assembly for automatically moving said syringe from said first linear conveyor to a filling position at said automated filling station under the control of said programmable controller; and a second linear conveyor in communication with said programmable controller and having a second shuttle movable therealong for automatically conveying said selected bulk medicine container from said bulk medicine container storage assembly to said automated filling station under control of said programmable controller; wherein said automated filling station further comprises a plurality of arms (110, 111, 112, 128) for manipulating said syringe, said plurality of arms (110, 111, 112, 128) each terminating in a forked end for engaging the syringe, and each arm (110, 111, 112, 128) being independently controlled and articulating along two axes to withdraw a plunger of said syringe to fill said syringe with medicine.