Bhutan (2010) and Rwanda (2011) were the first countries in Asia and Africa to introduce national, primarily school-based, human papillomavirus (HPV) vaccination programmes. These target 12 year-old girls and initially included catch-up campaigns (13-18 year-olds in Bhutan and ninth school grade in Rwanda). In 2013, to obtain the earliest indicators of vaccine effectiveness, we performed two school-based HPV urine surveys; 973 female students (median age: 19 years, 5th-95th percentile: 18-22) were recruited in Bhutan and 912 (19 years,[17][18][19][20] in Rwanda. Participants self-collected a first-void urine sample using a validated protocol. HPV prevalence was obtained using two PCR assays that differ in sensitivity and type spectrum, namely GP51/GP61 and E7-MPG. 92% students in Bhutan and 43% in Rwanda reported to have been vaccinated (median vaccination age 5 16, 5th-95th: 14-18). HPV positivity in urine was significantly associated with sexual activity measures. In Rwanda, HPV6/11/16/18 prevalence was lower in vaccinated than in unvaccinated students (prevalence ratio, PR 5 0.12, 95% confidence interval, CI: 0.03-0.51 by GP51/GP61, and 0.45, CI: 0.23-0.90 by E7-MPG). For E7-MPG, cross-protection against 10 high-risk types phylogenetically related to HPV16 or 18 was of borderline significance (PR 5 0.68; 95% CI: 0.45-1.01). In Bhutan, HPV6/11/16/18 prevalence by GP51/GP61 was lower in vaccinated than in unvaccinated students but CIs were broad. In conclusion, our study supports the feasibility of urine surveys to monitor HPV vaccination and quantifies the effectiveness of the quadrivalent vaccine in women vaccinated after pre-adolescence. Future similar surveys should detect increases in vaccine effectiveness if vaccination of 12 year-olds continues.National, primarily school-based, HPV vaccination programmes were started in Bhutan in 2010 1 and in Rwanda in 2011. 2 HPV6/11/16/18 vaccine coverage was reported as >90% in the target groups of both countries. In Bhutan, this target was 12 year-old girls, with a one-round catch-up campaign in 2010 for 13-18 year-old girls. In Rwanda, the target was girls attending primary school grade 6 (aged 12 years) in 2011, with three-rounds of catch-up vaccination in 2011, 2012 and 2013 for secondary school grade 3 (aged 15 years). Efforts were also made to reach out-of-school girls in health centres in both countries. 1,2 These two early-introducing countries provide the first opportunity to evaluate the impact of HPV vaccination in low/medium income countries (LMIC), of which the most feasible and informative measure in the medium-term (5-15 years) is type-specific HPV infection in sentinel populations of adolescent girls and young women. To this end, the International Agency for Research on Cancer (IARC) has developed long-term monitoring studies with the ministries of health of the two countries, beginning with two cervical cell surveys in the country capitals (Thimphu and Kigali) to establish robust baseline estimates of HPV prevalence among unvaccinated sexually activ...