OBJECTIVES: Millions of children younger than 5 years of age die every year due to malnutrition. Most of these children live in developing countries. The aim of this study is to describe malnutrition-mortality inequalities in children under five years from Colombian municipalities. METHODS: Mortality registers during 2000, 2005, 2010 and 2013 were extracted from the vital statistics of the National Administrative Department of Statistics (DANE, in Spanish) to estimate malnutrition-mortality rates per 100.000 children under five years (MMR<5) in the Colombian municipalities. MMR<5 were compared among groups determined by unsatisfied basics needs (UBN) quintiles as a proxy of poverty (Q1, Q2, Q3, Q4 and Q5, being the last one the poorest). RESULTS: Colombia registered 7,533 deaths caused by malnutrition between 2000-2013, wherein 47.3% of cases were girls. The MMR<5 was 15.5 and 6.1 per 100.000 for girls in 2000 and 2013, respectively. For the same years, the rates for boys were 19.3 and 7.3. MMR<5 was greater in boys than in girls in all years studied. At the municipal level, the MMR<5 for Q1 (less poverty) was the lowest for 2000, 2005, 2010 and 2013 in contrast with the others poverty quintiles. In boys, MMR<5 was 1.5, 4.7, 3.8, 3.5 times greater in Q5 versus Q1 (low poverty) for 2000, 2005, 2010 and 2013, respectively. In girls, the differences were 3.0, 3.5, 6.1 and 11.2.  CONCLUSIONS: Malnutrition mortality gaps have increased along the study period, especially in girls. Public health policies should be addressed to avoid malnutrition deaths in children under five years.