Theoretical population genetic studies of transposable elements focus almost exclusively on random mating species, whereas many plants reproduce through partial or substantial self-fertilization. Here I develop computer simulation and analytic approximations of simplified element dynamics (transposition balanced by selective elimination) in partially self-fertilizing populations, using Ty1-copia elements for biological inspiration. Under the most plausible models and parameter values, element numbers decrease with self-fertilization when element insertions are deleterious, but may increase when ectopic exchange regulates element number. Conclusions for models of ectopic exchange depend in part on parameters for which little firm empirical evidence is available. Small changes in selfing rate can lead to abrupt changes in element number when homozygous and heterozygous elements have markedly different fitness effects. Equilibrium element numbers can be sensitive to population size, especially at high selfing rates. Elements are frequently lost in small highly selfing populations under the deleterious insertion model. In contrast, small highly selfing populations can accumulate very large numbers of elements under ectopic exchange. Empirical data on element number and localization in plants with different mating systems suggests that deleterious insertion, rather than ectopic exchange, may regulate element number. Limitations to available empirical data, especially the lack of comparison between closely related species differing in mating system, mean that this conclusion is tentative.