Honduras has made steady progress in expanding post-primary school coverage in recent years, but many rural communities still do not provide a middle (lower secondary) school. As a result, Honduras has implemented a number of middle school alternative programmes designed to meet the needs of at-risk populations throughout the country. This article analyses dropout in three of the four main alternative lower secondary school programmes in Honduras over a three-year period for a cohort of roughly 5,500 students. The results show that these programmes are indeed reaching a vulnerable population in the country, but dropout rates are generally very high--upwards of 50 per cent in some cases--between Grades 7 and 9. Furthermore, even in the control school comparison samples made up of formal lower secondary schools, about 25 per cent of children leave school between Grades 7 and 9. The authors' analysis includes propensity score matching (PSM) methods that make more focused comparisons between students in alternative programmes and control samples. These results show that dropout rates in alternative programmes are not much different than in control schools, and only significant in one programme comparison, when taking into account family background characteristics like socioeconomic status (SES). Multivariate analysis within alternative programme samples finds that attrition is lower in those learning centres which have adopted key features of formal schools, such as university-educated teachers. The results highlight the tremendous variation in the alternative middle school sector in terms of programme features, school quality and student outcomes, as well as the challenges of expanding this sector to meet the growing demand for lower secondary schooling in Honduras.