Botswana is the world's second HIV heavily affected country, with an average HIV prevalence of 17.6% in 2013. The data used for this study are from Botswana AIDS Impact Surveys, I-IV, which are nationally representative sample surveys conducted in 2001, 2004, 2008 and 2013 respectively by the Central Statistics Office and the National AIDS Coordinating Agency. The purpose of this study was to investigate the levels, trends and factors associated with misconceptions about HIV transmission among adolescents. Both descriptive statistics and binary logistic regression analysis were used to address the study objectives. Overall the levels of HIV-related misconceptions among adolescents showed a declining trend over time, even though this trend is not consistent across the various misconception variables. The statistically significant factors influencing misconceptions were primary or lower education and being male in three surveys out of the four surveys. The study results show that despite major intervention aimed at behaviour change, myths and misconceptions about HIV transmission remain. Therefore, the intensification of the information, education and communication campaigns aimed at dispelling misconceptions are required, particularly aimed at the less educated and male adolescents.