There is substantial evidence that contraceptive side-effects are a major deterrent to consistent use of contraception but few studies in low- or middle-income countries explore the role that specific side-effects, rather than “side-effects and health concerns”, have on contraceptive dynamics. This study used population-based, longitudinal data to explore the effect that specific side-effects had on contraceptive continuation, discontinuation, and switching in Uganda. Methods Data for this study come from two rounds of PMA2020 data collection in Uganda PMA2020 Uganda’s sixth cross-sectional survey and a follow-up survey conducted one year later. The main outcomes of interest were discontinuation and switching among modern users of hormonal contraceptive methods and the IUD at baseline (n=550). Multivariable multinomial logistic regressions assessed the association of reporting experiencing specific side-effects (more bleeding, less bleeding, irregular bleeding, increased dryness/reduced libido, and physical discomfort) with discontinuation and switching one year later, adjusting for socio-demographic characteristics, type of method, and length of use.ResultsOne-third of hormonal contraceptive users reported experiencing side-effects at baseline. Reporting more bleeding increased the risk of discontinuation by 2.39 times (95% CI: 0.01-4.72). Experiencing irregular bleeding decreased the risk of switching by a factor of 0.40 (95% CI: 0.17-0.93). Vaginal dryness/reduced libido and physical discomfort were both marginally associated with increased relative risk of switching, increasing the risk of switching by a factor of 3.10 (95% CI : 0.97-9.10) and 1.75 (95% CI: 0.95-3.24), respectively. Wealth was significantly negatively associated with discontinuation while education was marginally significantly and positively associated with switching. ConclusionsGreater attention should be paid to understanding the unique contributions of side-effects to contraceptive behavior using population-based data. Not all side-effects are associated with contraceptive discontinuation and switching, despite the experience of side-effects being common. The experience of physical discomfort and vaginal dryness/reduced libido, largely ignored in other research, were shown to affect use. Providing greater individualized care that includes information about common side-effects and how they may impact daily life is necessary.