BACKGROUND The covid-19 pandemic has considerably affected the mortality numbers of many countries in the world, and Latin America is now the epicenter of the diseases. There is a great demand on analyzing the impact of this new disease in the amount of deaths, but available information of deaths by cause is still lacking in most of the countries in the region. OBJECTIVE We aimed to measure the effects of the disease on mortality, using excess mortality, in two Latin America countries that were most affected by the covid-19 pandemic in the region: Brazil and Ecuador. METHODS We measured the effects of the pandemic by looking at the excess mortality, and comparing estimates of differences in the average number of deaths, variation coefficients and percentages of deaths between the months of March to May for 2019 and 2020. RESULTS Our findings indicated an excess of deaths initially in major cities, but then is spreading towards the least urbanized areas. In the next phase, pandemic will probably affect countries’ cities in worse socioeconomic and sanitary conditions. In Ecuador, we saw that the most affected locations were the less socioeconomic areas of the country. CONCLUSION Despite the lack of information on causes of death, the excess of deaths is a good indicator for measuring the effects of the coronavirus pandemic, especially in the context Latin America countries. We find strong evidence of the pandemic’s impact and interiorization, especially in Brazilian cases. CONTRIBUTION This study provides an initial discussion of the effects of pandemic in small and less urbanized areas of Brazil and Ecuador.