Plants have developed several genetically regulated defense strategies against a wide range of biotic stresses (viruses, fungi, bacteria, nematodes). There is experimental evidence that DNA methylation and post-transcriptional gene silencing (PTGS) are strongly associated and have evolved as plant defense mechanisms against invasion by foreign nucleic acids, including viruses. Recent studies have shown that PTGS is activated in plants infected by the geminivirus Tomato yellow leaf curl Sardinia virus (TYLCSV). To compare the DNA methylation profiles in TYLCSV-infected vs mock-inoculated tomato (Solanum lycopersicum syn. Lycopersicon esculentum) plants, a methylation-sensitive amplification polymorphism (MSAP) methodology was applied. The pattern of methylation was assayed at different stages of infection (1, 7, and 14 days) after inoculation by the natural vector Bemisia tabaci. Thirty-four polymorphic fragments were identified, of which ten were sequenced. The majority (eight out of ten) of polymorphisms generated by changes in methylation after TYLCSV infection belong to expressed portions of the tomato genome, mostly involved in defense and stress responses. Although the differences in expression levels during infection (in all cases examined except one) could be detected at least at one time-point, no clear correlation could be found between overexpression or underexpression and changes in methylation profiles. Our data demonstrate that TYLCSV induces changes in the methylation status of the tomato genome and that MSAP might contribute in identifying genes involved in plant–virus interactions.