Aim: To examine the relationships between island environmental attributes, both biotic and abiotic, and three measures of reptilian variation – species assemblage, species richness, and body size distributions. Location: Houtman Abrolhos archipelago, Western Australia. Taxon: Reptiles. Methods: Nineteen islands were sampled from 2002 - 2012 using foraging and trapping. Body size (snout-vent length) was measured on first capture. Island size varied from 0.3 - 587 ha, encompassing the three geomorphic island types, the three bathymetric groups, and a range of other environmental attributes. Results: From about 1500 captures, 24 reptile species were recorded, including three previously undocumented on the archipelago, and 55 records of species not previously recorded on specific islands. Four significantly different reptile assemblage groups were identified. These were highly correlated with geomorphological composition - two groups encompassing the three large aeolianite islands; another the high rock islands and the largest composite island; and a fourth consisting of the remaining composite islands with one very small high rock island. Both assemblage and richness on islands were significantly correlated with island area, geomorphology and native plant species richness. Of the 13 species captured frequently, eleven showed statistically significant inter-island variation in body size, and two exhibited sexual dimorphism. In three species, size was also correlated with environmental attributes, including reptile species richness, native plant richness, geomorphology and island area. Six of the eleven species captured on the two largest islands (both aeolianite) differed in size on these adjacent islands. Main Conclusions: High inter-island variation in body size and assemblage composition suggest strong differential selection since the most recent isolation event at 6,500 bp. Anthropogenic disturbances over the last 150 years have resulted in several island extinctions. Species assemblage and richness are strongly associated with environmental attributes. Inter-island body size variation in three species revealed idiosyncratic responses to environmental pressures. Results provide guidance for effective conservation and management strategies, and evidence for the extinction debts inherent in more recently fragmented mainland habitats.