The most common transposable genetic element in humans, long interspersed 
element 1 (L1), constitutes about 20% of the genome. The activity of L1 and 
related transposons such as Alu elements causes disease and contributes to 
speciation. Little is known about the cellular mechanisms that control their 
spread. We show that expression of human APOBEC3B or APOBEC3F decreased the rate 
of L1 retrotransposition by 5-10-fold. Expression of two related proteins, 
APOBEC3D or APOBEC3G, had little effect. The mechanism of L1 inhibition did not 
correlate with an obvious subcellular protein distribution as APOBEC3B appeared 
predominantly nuclear and APOBEC3F was mostly cytosolic. Two lines of evidence 
indicated that these APOBEC3 proteins use a deamination-independent mechanism to 
inhibit L1. First, a catalytically inactive APOBEC3B mutant maintained L1 
inhibition activity. Second, cDNA strand-specific C --> T hypermutations were 
not detected among L1 elements that had replicated in the presence of APOBEC3B 
or APOBEC3F. In addition, lower levels of retrotransposed L1 DNA accumulated in 
the presence of APOBEC3B and APOBEC3F. Together, these data combined to suggest 
a model in which APOBEC3B or APOBEC3F provide a preintegration barrier to L1 
retrotransposition. A particularly high level of APOBEC3F protein in human 
testes and an inverse correlation between L1 activity and APOBEC3 gene number 
suggest the relevance of this mechanism to mammals.