Background Many studies examine the use of medicines among pregnant women, however few studies report the pregnant women's belief for taking medication during pregnancy. Individual factors such as patients' beliefs about their medications have been known to influence medication adherence. Objective This study aimed to examine beliefs about medicines among pregnant women in Indonesia and how these varied across pregnancy trimesters. Setting We conducted a cross-sectional survey of pregnant women who had regular visits at 63 community health centres in Surabaya, Indonesia. Methods Participants were approached while they were in the waiting room and were asked to complete the questionnaire. The survey package contained information about the study, an informed consent form, and the Beliefs about Medicines Questionnaire (BMQ). Main outcome measure Beliefs about medicines were assessed using the BMQ, which comprises four subscales: general-overuse, general-harm, specific-necessity, and specific-concern. Differences in medication beliefs between pregnancy trimesters were assessed using suitable statistical tests according to data normality. Results A total of 492 pregnant women completed the survey. The majority were aged 21-30 years (57.1%), housemakers (68.7%), and educated to high-school level (51.4%); 92.9% did not have any chronic diseases, and more than 90% took vitamins and/or supplements. The difference between Specific-Concern and Specific-Necessity scores was calculated for each participant, and more than half of the participants (59.6%) were thus classified as having negative beliefs about medications. In the first trimester of pregnancy, women's beliefs about medication necessity were stronger than in the third trimester (p = 0.033). Conclusion Medication beliefs of pregnant women regarding their concerns and the necessity of medication taken in different trimesters of pregnancy were varied. The results of this study highlight the difference in medication beliefs during trimesters in pregnancy.