In this study presents materials and design optimization of clinically approved hydroxyapatite (HA) using extrusion based 3D printing process. The effect of various printing parameters including print speed, extrusion pressure, accuracy and infill density to produce defined porous structures is established using various techniques. Particularly Scanning Electron Microscopy, Micro Computed Tomography have been employed to study internal and external accuracy. Mechanical testing was employed to study the effect of porosity on compressive properties of 3D printed structures. This study shows that, the infill density and shrinkage of 3D printed HA scaffolds post sintering have a linear relationship. Porosity and mechanical strength of 3D printed scaffolds depend on the infill density of the designed CAD file. Tailoring infill density also helps in altering mechanical properties in a predictable manner. Finally, a case study on hydroxyapatite printing of a patient specific bone graft demonstrates the ability of this material and technique to print complex porous structures created on CT-based anatomical bone models and pre-operative 3D planning, providing further promise for custom implant development for complex bony designs. © 2018 The Authors