Diarrheal diseases are the second leading mortality cause of death in children under five years old. The purpose of this study was to describe diarrheal mortality inequalities in children under five years. Vital statistics from National Administrative Department of Statistics (DANE, in Spanish) were used to estimate diarrheal mortality rates per 100.000 children under five years (DMR<5) in the Colombian municipalities with mortality registers during 2000, 2005, 2010 and 2013. DMR<5 were compared between groups determined by unsatisfied basics needs (UBN) quintiles as a proxy of poverty (Q1, Q2, Q3, Q4 and Q5, being the last the poorest). Between 2000 and 2013, Colombia registered 7,214 deaths in children under five years caused by diarrheal disease, 44% of cases were girls. Colombian DMR<5 was greater in boys for all the years. The DMR<5 for Colombian boys in 2000 and 2013 was 23.4 and 3.9 per 100.000, respectively. For girls, the DMR<5 was 22.2 and 2.9 for the same years. At the municipal level, DMR<5 for Q1 (less poverty) was the lowest for 2000, 2005, 2010 and 2013 versus other poverty quintiles. In boys, DMR<5 was 2.3, 3.7, 10.8 and 15.7 times greater in quintiles with high poverty (Q4 and Q5) versus Q1 (low poverty) for 2000, 2005, 2010 and 2013, respectively. In girls, the differences were 3.1, 5.8, 15.8 and 21.5. Although diarrheal mortality rate has decreased during the study period, the diarrheal mortality gap has increased among Colombian municipalities.