Natural cerrado vegetation in São Paulo State now covers less than 7% of its original area and exists only as isolated fragments. Eighty-six sites in these priority cerrado conservation areas were surveyed using a rapid assessment technique. A total of 554 species of vascular plants, belonging to 77 families, was recorded. The vegetation types encountered comprised: campo sujo, campo cerrado, cerrado sensu stricto, cerradão, wet campo, riparian forest, swamp forest, ecotone cerrado/forest and seasonal semi-deciduous forest. Two-Way Indicator Species Analysis (TWINSPAN), Detrended Correspondence Analysis (DCA) and Unweighted Pair-Groups Method using Arithmetic Averages (UPGMA) revealed a weak similarity pattern based on geography, but divided the sites into two main structural groups: (a) areas where more open forms of cerrado occur (cerrado sensu stricto, campo cerrado); (b) areas where only forest physiognomies occur (cerradão, ecotone cerradão/seasonal semi-deciduous forest, or riparian forest). The first group tends to be located in the east and the second in the west of São Paulo State. Cerradão was the most frequent vegetation type, observed in 70% of the sites. Cerrado sensu stricto was recorded in only 31% of the sites. Casearia sylvestris and Byrsonima intermedia were the most widespread species, recorded in 90% and 88% of the sites, respectively. Only 10% of the species were found in 50% or more of the sites, while 19% of species were recorded at a single site only. There was a considerable difference in species number between sites, from a minimum of 29 at Taubaté to a maximum of 185 in one of those at Campos Novos Paulista. As shown in other studies, species richness is directly correlated with diversity of vegetation types occurring at a site (beta diversity). As expected, the seven richest fragments contain ecotonal vegetation, which combines both forest and cerrado elements.