Background: Sikkim is a northeastern state of India, located in the Himalayas with migratory population from neighboring states and Nepal. Although there is high prevalence of human immunodeficiency virus (HIV) and Hepatitis B and C virus (HBV and HCV) in other northeastern states of India, currently, this information is lacking in Sikkim’s adolescent population, which inspired the researchers to conduct this study. Methods: This is a cross-sectional study with 490 adolescent participants between the age group of13–20 years. Schools/colleges and the participants were randomly selected. Blood samples of selected participants were collected after their interview and were tested for anti- HIV, hepatitis B surface antigen and anti-HCV. Findings: Mean age of the participants was 16.96 years. Only 1 (0.2%) participant was positive for HBsAg and none was positive for anti-HIV and anti-HCV. About 92 (18.78%), 90 (18.37%), 79 (16.12%) and 12 (2.45%) participants had respectively undergone tattoo/body piercing, invasive (medical) procedure, shared personal items and had received blood transfusion but none of them provided information on their use of injectable drugs. A total of 33 (6.73%) participants expressed their involvement in heterosexual relation, of which 29 (29/215, 13.49%) were boys and 4 (4/275, 1.45%) were girls (p<0.01). Among them, 13(13/33, 39.39%) participants expressed their involvement with multiple sexual partners and16 (16/33, 48.49%) participants had taken protective measures. None of the girls provided history about their partner taking any protective measures. Interpretation: To the best of our knowledge, this is the first study reporting on the prevalence of HIV, HBV and HCV in the adolescent population of Sikkim. Our results indicate that there is a very low prevalence of HBV and absence of HIV and HCV infections in the studied population. However, the studied population is at risk of acquiring these infections and therefore necessary steps must be taken to prevent the transmission of these viruses. Funding: Indian Council of Medical Research.