The role of the public transport system as promoter of social inclusion is gaining increasing attention in the fields of transport policy and planning. This is especially relevant in areas traditionally characterized by high levels of poverty and structural inequalities where it can be a decisive element in the reduction of social exclusion. This paper evaluates the topic through an innovative methodology based on index comparison. Firstly, a traditional accessibility index is used which considers the access time to public transport stops, and secondly an Index of Transport Social Disadvantage is proposed. It includes the transport disadvantage factors of the populations, such as disability, old age, low income, unemployment and pre-school children. These transport disadvantage characteristics have been divided into two groups: the first includes the disadvantage characteristics distributed equally. In the second group, the disadvantaged groups in transport with an unequal territorial distribution are taken into account. The Gini index is used to ascertain the differences in these groups. This method facilitates the identification of the unequal distribution of transport disadvantage and therefore, social exclusion. The consideration of the two indexes, access time and transport social disadvantages, will find the areas not only with low accessibility levels, but also with high levels of population with transport disadvantages, thereby assessing social exclusion linked with public transport. This methodology is applied to the public operated transport system of the Guadalajara Metropolitan Area, Mexico. Its development reveals which areas are affected by the under provision of public transport as well as the population characterized by transport social disadvantage, which together give a clear indicator of the situation of social exclusion linked to the public transport system.