The road network has both positive and negative ecological effects, and understanding these helps identify environmentally preferable solutions for transportation policy and planning. We investigated the relationship between road density and habitat type richness of Greek protected areas. We used digital vector maps of 214 sites included in the Greek Natura 2000 network. We calculated road density for the terrestrial part of each site and correlated it with habitat type richness. Average road density of protected areas (0.377 km/km2) was significantly lower than the national road density of Greece (0.446 km/km2). We identified 32 sites that were not intersected by roads. These roadless sites were located at mountain tops, at islets, or in remote coastal zones. Overall we found no significant correlation between road density and habitat type richness. We suggest that the effect of road networks on habitat type richness is less apparent at landscapes with long history of human presence, because the landscape (and its habitat diversity) has coevolved with human activities over the past millennia. Our analysis provides a step towards quantifying the effect of road density on the diversity of habitats and consequently on species of conservation interest in international networks of protected areas such as the European Natura 2000 network.