The term inbreeding refers to any form of mating that involves genetically similar or related organisms, whether intentional or not. While inbreeding does not change the frequency of the alleles in a population, it does redistribute genotypes, and increase consanguinity and homozygosity, ultimately decreasing levels of genetic diversity in a population. One of the principal consequences of inbreeding is inbreeding depression, which is a reduction in the evolutionary fitness of the individuals that make up a population. Although inbreeding may often lead to a decrease in the reproductive success of a group of organisms, it also represents a potentially useful tool for the isolation and retention of a desired trait in breeding programs of both plants and animals. Inbreeding can occur naturally in the wild, and will contribute to the propagation of a species, although its effects can vary considerably between large, randomly-sorted populations and small, isolated populations. In small populations, inbreeding can have drastic consequences, such as the rapid manifestation of undesirable traits, including the expression of deleterious alleles or the acquisition of traits that decrease reproductive success. This chapter addresses the causes and effects of inbreeding, and discusses biological concepts, such as the coefficient of endogamy, inbreeding depression, and the consequences of reduced heterozygosity, using populations of neotropical organisms as examples.