Healthcare waste is a major public health hazard in developing countries. The aim of this study was to assess healthcare waste management (HCWM) system currently employed in selected healthcare facilities (HCFs) in Madagascar.Data was collected through a questionnaire and field visit in 2009. Seventeen HCFs were randomly selected from seventy six HCFs whose staff had undergone HCWM in 2006. The quantity of infectious waste generated per day at the HCFs was in proportion to the number beds (r= 0.838 and p<0.05). Non-sharps infectious waste was positively correlated with sharps (r=0.709, p=0.001). The availability of waste management plan was reported in 52.9% while the implementation of color coding system for waste segregation was reported in 76.5% HCFs. Waste segregation was reported by majority of HCFs (82%). Moreover, the most common disposal method was Montfort incinerator (65%). In general, there was improved HCWM system in HCFs surveyed, although certain HCFs still had poor management due to inadequate infrastructure and equipment for segregation, collection, transport, and disposal of medical waste (MW) as well as poor waste generation records. Interventions strategies should include adherence to national regulatory framework, periodic training and sensitization of healthcare worker and increased allocation of resources for HCWM.