We describe the distribution and diversity of vascular plants at high elevations (3980–4570 m above sea level) in the Rwenzori Mountains and Mount Elgon National Parks in Uganda. These were the first target regions of the “Global Observation Research Initiative in Alpine Environments” (“GLORIA”) on the African continent. In each target region, four summits spanning elevations from the treeline ecotone up to the limits of vascular plant life were selected and assessed in July and August 2011 using the standardised GLORIA protocol. Few vascular plant species were present on high elevation summits, particularly in Rwenzori, where many sub-plots had little or no vascular plant cover. Observations from Rwenzori include 26 vascular plant species, and from Mount Elgon 47, of which 10 and 15 species, respectively, were endemic. In contrast, non-vascular plant cover greatly increased with elevation. The lowest sites showed considerable diversity and were floristically dissimilar to the highest summits. Subsequent resurveys, repeating the GLORIA protocol, will be critical in the assessment of ongoing dynamics and change.