BackgroundIn Uganda, the risk of unintended pregnancies and unsafe abortions remains high due to relatively low contraceptive use. There is paucity of data on knowledge, attitudes, perceptions and practices towards modern contraceptives and, sexual and reproductive health especially among the young female university students.MethodsA survey was conducted at Makerere University main campus in Kampala, Uganda during April 2014. A team of well-trained and experienced research assistants interviewed female undergraduate students who provided data on socio-demographic characteristics, knowledge, perceptions and attitudes and use of contraceptives, as well as other sexual and reproductive health practices. Users of any contraceptive method in the past 12 months were coded as ‘1’ and none users as ‘0’. The prevalence of contraceptive use was determined as the number of users divided by all female participants. Prevalence ratios (PRs) with their corresponding 95 % confidence intervals were used as measures of association between contraceptive use and associated factors. The PRs were obtained via a modified Poisson regression model using a generalized linear model with Poisson as family and a log link without an offset but including robust standard errors. All analyses were conducted with Stata version 13.ResultsA total of 1,008 females responded to the survey; median (IQR) age was 21(20, 21) years, 38.6 % in year 2 of study, and nearly three quarters (72.3 %) were of Christian faith. Knowledge of any contraceptives was almost universal (99.6 %) but only 22.1 % knew about female condoms. Perceived acceptability of contraceptive use at the university (93 %) or being beneficial to male partners too (97.8 %) were high. Nearly 70 % had ever engaged in sexual intercourse and 62.1 % reported sexual intercourse in the past 12 months. Overall, 46.6 % reported current contraceptive use, with male condoms (34.5 %) being the commonest methods. Factors associated with higher contraceptive use were being in year 2, consensual union or perception that contraceptives are for females only. However, being evangelical/SDA or perception that contraceptive use is wrong was associated with lower contraceptive use. Overall, 9 % reported ever being pregnant, 2 % were pregnant at the time of the survey and a third (33.8 %) knew of a pregnant friend. About 40 % of ever pregnant respondents reported ever trying to terminate the pregnancy.ConclusionsKnowledge, perceived acceptability and benefits of contraceptive use were nearly universal, but contraceptive use was suboptimal in this setting. Ever trying to terminate a pregnancy was common and a clear indicator of unintended pregnancies.