Background: The objective of this study was to establish a regional profile of the indigenous knowledge system (IKS) for medicinal plant use and cultural practices associated with the healing process of these plants by traditional healers in the Oshikoto region, Namibia. Methods: An ethnobotanical survey was undertaken to collect information from traditional healers during September and October 2008. Data was collected through the use of questionnaires and personal interviews during field trips in the ten constituencies of the Oshikoto region. A total of 47 respondents were interviewed with most of them aged 66 and above. Results: The traditional healers in Oshikoto region use 61 medicinal plant species that belong to 25 families for the treatment of various diseases and disorders with the highest number of species being used for mental diseases followed by skin infection and external injuries. Trees (28 species) were found to be the most used plants followed by herbs (15 species), shrubs (10 species) and climbers (4 species). The average of the informant consensus factor (F_IC) value for all ailment categories was 0.75. High F_IC values were obtained for Pergularia daemia, and Tragia okanyua, which were reported to treat weakness and dizziness problems, snake bite, swelling and cardiovascular problems indicating that these species traditionally used to treat these ailments are worth examining for bioactive compounds. Conclusions: The traditional healers in Oshikoto possess rich ethno-pharmacological knowledge. This study allows for identifying many high value medicinal plant species, indicating high potential for economic development through sustainable collection of these medicinal plants.