Objectives Standard indicators are being used worldwide to track progress towards achieving the Millennium Development Goals (MDGs). These are usually at country level and do not accurately reflect within-country variability of progress towards the targets. This may lead to lack of attention and under-resourcing of the most vulnerable populations. Therefore, the objective of this study was to compare selected standard MDG indicators at country level and community level in Peru. Methods As MDG indicators we selected: (i) moderate to severe and severe underweight in children under 5 years old; (ii) immunization against measles in 1-year olds; (iii) births attended by skilled health professionals and (iv) youth unemployment. Country-level data for Peru were obtained from United Nations published sources. Community-level data were obtained from a household survey conducted in 2005-2006 in Belén, a community of extreme poverty in the Amazon region. Results Belén indicators were consistently less favourable than country-level indicators, and indicators even differed between zones of high and low socioeconomic status within Belén itself. Conclusions Compared to MDG indicators at the national level in Peru, the population of Belén experiences intra-country regional disparities in important health and social outcomes. Improving the coverage and quality of interventions and services in this community is essential. Other vulnerable populations in Peru should also be identified and targeted so that they can benefit from, and ultimately contribute to, progress in achieving the MDGs.