Bacterial contamination of contact lenses (CLs) may contribute to CL-related corneal infection and inflammation. This study reports CL biota over time during daily and extended wear. Microbial contamination of a 58% water, ionic hydrogel CL and a 38% water, non-ionic hydrogel CL was evaluated in an Australian and an Indian population. Fifty wearers were repeatedly sampled over 18 months. Overnight CL use did not alter the frequency of positive cultures, nor the spectrum of organisms compared with daily CL wear. There were no differences in type and frequency of CL contamination between the CL types. Positive cultures were more frequently recovered from the Indian population compared with the Australian population. Streptococcus spp. and Propionibacterium spp. were more frequently isolated from the Australian population. Fungi and Bacillus spp. were more frequently isolated from the Indian population. Normal CL biota alone cannot explain the increased rate of infection and inflammation in extended wear.