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Objective: Malaria is a major cause of morbidity and mortality in tropical and subtropical regions, affecting mostly the impoverished sections of the population. Pregnant women living in malaria-endemic areas are at higher risk of malaria infection with higher density of parasitaemia than non-pregnant women. The aim of this study was to assess factors affecting the uptake of IPT among women attending antenatal clinics at Bondo District Hospital, Western Kenya., Methods: This study was a hospital-based cross-sectional survey among pregnant women attending clinics. Malaria is endemic in Bondo district. Both women from Bondo town (urban) and greater Bondo District (rural) who had been pregnant for at least 35 weeks or had delivered not more than 6 weeks prior to the survey), and had ANC cards were included in the study. The main outcomes were ANC attendance, IPT doses received and client and provider factors., Results: Results showed that women's knowledge on ANC and IPT was high. The uptake of IPT was low among pregnant women with those from urban areas more likely to make more ANC visits and to get more IPT doses than women from the rural areas. ANC attendance was hampered by the fear of being tested for HIV at the clinic. Perceived side effects associated with IPT-SP hindered IPT uptake and were linked to HIV-related symptoms. Negative attitude among health workers towards pregnant women also adversely impacted IPT uptake. Women suggested that IPT drugs be distributed through community health workers instead of the health facility for improved uptake., Conclusions: Retraining of health workers on the administration of IPT, harmonization of health messages, and assessment of alternative community-based IPT distribution channels ought to be urgently considered. More evidence on the influence of HIV pandemic on perceptions and attitudes toward and uptake of other health interventions is urgently needed.