In 2014, a population based cross sectional study was conducted to determine the prevalence of trachoma and associated risk factors in the Lower Shire Valley of Southern Malawi. A total of 2,957 children aged 1-9 years who were assessed for clinical signs of trachomatous inflammation – follicular (TF) and 2,247 adults aged 15 and above were assessed for signs of trachomatous trichiasis (TT). The prevalence of TF among children aged 1-9 years was found to be 18.5% (95% CI 16.4-20.8) in Nsanje and 7.8% (95% CI 6.6-9.2) in Mwanza districts respectively. The prevalence of TT in adults aged 15 and above was 0.5% (95% CI: 0.1-0.9) in Nsanje district and 0.2% (95% CI: 0.1-0.4) in Mwanza district, respectively. In regards to risk factors, only the presence of a dirty face was associated with trachoma follicular (TF) in Nsanje and Mwanza districts (P< 0.001). The prevalence of trachoma in Nsanje suggests the need for the implementation of the full SAFE (Surgery, Antibiotics, Face Washing and Environmental) control strategy.