The aim of this study was to identify the main on-farm welfare issues likely to be encountered in extensive sheep farming systems. Thirty-two commercial sheep farms in Victoria, Australia were involved in this study. Of the 32 farms involved, 30 were visited twice (at mid-pregnancy and weaning), and 2 farms only once (both at weaning). In total, 62 visits were conducted and 6,200 ewes (aged 2-5 years) were examined using six animal-based indicators: body condition score (BCS), fleece condition, skin lesions, tail length, dag score and lameness. In addition, the number of ewes that needed further care (such as sick or injured sheep) was recorded and reported to the farmers. Generalised linear mixed models were conducted to investigate associations between welfare outcomes and visit, ewe breed and location, with all three, and their interactions, as fixed factors. In all instances, farm was set as a random factor to account for specific variation between farms. Overall, the welfare of the ewe flocks, based on the six indicators measured, was considered good. A total of 86.9% of the ewes were in adequate BCS (2.5-3.5), 91% had good fleece condition, 69.2% had no skin lesions, 97.1% had low dag scores, and overall lameness was 4.7%. An important and prevalent risk to welfare identified across farms was short tail length; with 85.7% of ewes having tails docked shorter than the third palpable joint. While the welfare of the flock was good, ewes in need of further care were identified at all farms. There were 185 (3.0%) cases needing further care, and the extent of welfare compromise of these animals was considered significant. Main reasons for further care were moderate/severe lameness or foot-related issues, BCS ≤ 2 and active dermatophilosis or broken wool. To our knowledge, this study constitutes the largest assessment of ewes conducted in Australia, and the findings provide valuable insight into the main welfare issues likely to be encountered in extensive sheep farming enterprises. Future studies should develop practical technologies that can assist in the detection of the welfare issues identified in this study. In addition, the thresholds identified here could be used for future comparison and sheep welfare benchmarking programs to assess farm performance and measure continuous improvements.