Introduction: Menstruation is culturally stigmatized natural biological event. In Uganda, adolescent girls in primary and secondary schools miss school due to menstruation. This baseline study was conducted to assess perception and practices of adolescents aged 9-17 years in rural primary and secondary schools in Jinja and Mayuge districts. Methodology: The survey used a descriptive design employing both quantitative and qualitative methods of data collection. A total of 1102 adolescents, Senior Women Teachers (12), Senior Men Teachers (4), two school administrators (2) and five (5) female parents of adolescent girls were included in the study using a simple random and purposive sampling methods. Permission and informed consent was first sought before collecting data from respondents. Primary data collection was conducted using a pre-tested semi-structured questionnaire, interview guides and Focus Group Guides (FGD). Collected data was entered into the Statistical Package for Social Scientists (SPSS), where it was analyzed using descriptive statistics. Results: Survey findings showed that most adolescents had poor knowledge about menstruation. Nineteen percent of adolescent girls aged 10-14 had never heard the word menstruation, 55.9% did not know how or why women/girls undergo menstruation, 94.5% did not know the source of menstrual blood, while 30.6% of girls and most boys in FGD believed that menstruation is a disease/curse. The major sources of information about menstruation were senior women teachers (SWT) (32%) and mothers (31.9%). Besides providing inadequate and incorrect information to adolescent girls, mothers and teachers were an indirect source of self-stigmatizing beliefs and views about menstruation. Most girls (39.9%) were using pieces of cloth to manage menstrual flow. Other materials used included sanitary pads, cotton wool, homemade reusable pads, reusable pads donated by NGOs, 2 panties, toilet paper, sitting in the sand and local herbs.