Objective: Examine patterns of contraceptive use among reproductive age women, with and without chronic disease, and investigate factors which influence contraceptive use over time. Design: Population-based cohort study Setting and population: Data from 8,030 women from the Australian Longitudinal Study on Women’s Health. Main outcome measures: Contraceptive patterns identified using latent transition analysis. Methods: Multinomial mixed-effect models were used to evaluate the relationship between contraceptive combinations and chronic disease. Results: Women with chronic disease used contraception at similar rates to women without chronic disease however contraceptive non-use increased over the observation period (13.6% vs 12.7% in 2018 when aged 40-45 years). When specific contraceptive use patterns were examined over time, differences were found for women with autoinflammatory diseases only. Compared to women without chronic disease using the pill and condoms, women with autoinflammatory disease had increased odds of using condom and natural methods (OR=1.20, 95% CI=1.00, 1.44), and sterilisation and other methods (OR=1.61, 95% CI=1.08, 2.39) or no contraception (OR=1.32, 95% CI=1.04, 1.66), compared to women without chronic disease using short-acting methods and condoms. Conclusion: Potential gaps in the provision of appropriate contraceptive access and care exist for women with chronic disease, particularly those diagnosed with autoinflammatory conditions. Development of national guidelines as well as a clear coordinated contraceptive strategy from adolescence through to the mid reproductive years and perimenopause encouraging regular contraceptive review during care management to increase support for, and agency among, women with chronic disease is required.