A porous structure comprises pores and pore throats with a complex three-dimensional (3D) network structure, and many investigators have described the relationship between average pore size and the amount of bone ingrowth. However, the influence of network structure or pore throats for tissue ingrowth has rarely been discussed. Four types of bioactive porous titanium implants with different pore sizes and porosities (6mm in diameter and 15 mm long) were analyzed using specific algorithms for 3D analysis of interconnectivity based on a micro focus X-ray computed tomography system. In vivo histomorphometric analysis was performed using the very same implants implanted into the femoral condyles of male rabbits for 6 and 12 weeks. This matching study revealed that more poorly differentiated pores tended to have narrow pore throats, especially in their shorter routes to the outside. In addition, for assessment of the entire implant, we proposed new two indices that represent the degree of bone and tissue ingrowth into an implant by considering the effect of narrow pore throats. Data obtained suggest that this sort of novel analysis is useful for evaluating bone and tissue ingrowth into porous biomaterials.