Small mammal ecology and natural history are poorly known in Nuclear Central America. In an effort to gain information on small mammals (insectivorans, marsupials, and rodents), we sampled three cloud forest habitats in mountain ranges in Honduras (Cerro Celaque and Sierra de Agalta) and Guatemala (Sierra de las Minas). Small mammals were collected using removal trapping. A total of 789 specimens representing 23 species of small mammal was recorded from seven trapping sites. Trapping effort varied among sites, with a total of 18,117 total trap nights recorded. We describe the habitat at each trapping site, and report on species diversity, relative abundance, sex ratios, reproductive activity, and other natural history information on the mammals collected. In general, cloud forests in the three mountain ranges contained different communities of small mammals. We recorded only three species, Heteromys desmarestianus Gray, 1862, Peromyscus oaxacensis Merriam, 1898, and Scotinomys teguina (Alston, 1877), on all three mountain ranges.