To examine breast cancer (BC) incidence trends in relation to mammographic screening and risk factor prevalence in South Australia (SA). Trends in annual BC incidence rates were calculated using direct standardisation and compared with projected incidence derived from Poisson regression analysis of pre-screening rates. Annual percentage change and change time points were estimated using Joinpoint software. Biennial mammography screening participation rates were calculated using data from BreastScreen SA. Trends in overweight/obesity, alcohol use and hormone replacement therapy (HRT) use were examined using 1991-2009 Health Omnibus Survey data. Trends in total fertility were examined using data from the Australian Bureau of Statistics. BC incidence increased around the time BreastScreen commenced and then stabilised in the mid-1990s. However rates have remained higher than projected, even though the proportion and age distribution of first time screening attendees stabilised around 1998. A decrease in BC incidence was observed among women aged 50-59yrs from the late-1990's but not among older women. Obesity and alcohol use have increased steadily in all age groups, while HRT use declined sharply from the late-1990s. BC incidence has remained higher than projected since mammography screening began. The sustained elevation is likely to be due to lead time effects, though over-diagnosis cannot be excluded. Declining HRT use has also impacted incidence trends. Studies using individual level data, which can account for changes in risk factor prevalence and lead time effects, are required to evaluate 'over-diagnosis' due to screening.