Background Due to the heavy patient-load and various types of services, the public health facilities produce a bulk of medical wastes (MW) in Bangladesh. Improper disposal of MW increases the risk of infection among the healthcare service personnel, patients, and attendants. The current study aimed to assess the practices of MW management and quantify those to find out the gaps in the specific steps of waste management.Methods As part of a larger intervention study, a facility assessment was conducted during November 2015 to March 2016 at a District Hospital (DH) and a Mother and Child Welfare Centre (MCWC) both being located in the same district, Non-participatory observation of MW management was done using a checklist developed following the Guideline for Medical Waste Management of Bangladesh. Scoring was applied for various activities of MW management performed in the study facilities.Results The overall scores in bin management, segregation, and collection of wastes were 64.5%, 58.1%, and 62.0% in the DH and 53.1%, 41.5%, and 48.0% in the MCWC respectively. The performance of operation theatre in MCWC was the lowest among different corners (16.7–36.0%). Re-usable waste was segregated poorly (32% in DH and 0% in MCWC), and almost none was shredded (4% in DH and 0% in MCWC). The wastes were transported from in-house to out-house temporary storage area in open-bin without any trolley or specific route. Storage area was accessible to unauthorized persons, e.g. waste-picker in DH. While DH segregated 84% of its infectious wastes at source, they eventually got mixed-up with other wastes in the storage area and delivered to municipality for dumping. MCWC could segregate only 40% of its infectious wastes at source and disposed those, using pit method. Both the facilities disposed sharp medical wastes by open-air burning and liquid wastes through sewerage without any treatment.Conclusions The performance of MW management was poor in both the study facilities. Advocacy to the healthcare personnel and refresher training, along with supportive supervision and monitoring, may improve the situation. Moreover, larger study is needed to find out the reasons behind such poor MW management.