BACKGROUND: The needle exchange programme (NEP) started in Sweden in 1986 in Lund and shortly after in Malmo. The first NEP in Stockholm opened in spring 2013. The NEP is a service aimed at intravenous drug users (IDU) from 18 years old, with a goal of preventing the blood borne diseases, such as HIV, Hepatitis B (HBV), and Hepatitis C (HCV). With the on going HIV and Hepatitis epidemics, numerous countries around the world have adopted control strategies, such as the NEP to halt the spread of HIV, HBV, and HCV. The objective of this study was to examine if the needle exchange programme has decreased the incidence of HIV, HBV, and HCV in Sweden over a six-year period.  METHODS: Data for incidence and prevalence was extracted from the yearly reports of the Stockholm’s needle exchange programme from 2013 to 2018 and the yearly reports of the public health agency in Sweden from 2013 to 2018. The data was collected for Stockholm, and compared to Västra Götaland, and the whole of Sweden. RESULTS: The incidence of HIV was zero in 2013 and 2015 in the NEP. The incidence of HBV decreased to zero in 2013 in the NEP. There is an increased incidence of HCV in the NEP. CONCLUSION: The NEP has a protective effect through its combination of needle exchange, opiate substitute therapy, counselling, and vaccinations in reducing and stabilising incidences of the infections, in some instances to zero, as well as providing surveillance and treating infections.