A porous structure comprises pores and pore throats with a complex three-dimensional 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. Bioactive porous titanium implants with 48% porosity were analyzed using specific algorithms for three-dimensional analysis of interconnectivity based on a micro focus X-ray computed tomography system. In vivo histological analysis was performed using the very same implants implanted into the femoral condyles of male rabbits for 6 weeks. This matching study revealed that more poorly differentiated pores tended to have narrow pore throats, especially in their shorter routes to the outside. Data obtained suggest that this sort of novel analysis is useful for evaluating bone and tissue ingrowth into porous biomaterials.