Current research has determined that many cloned animals have heterogeneous DNA methylation profiles. However, few studies have compared the methylation profiles of both naturally produced lambs and cloned lambs created using somatic cell nuclear transfer. The paucity of research in this area is because of insufficient resources to study limited cloned offspring, the ovine genome, and ovine genomic imprinting. In this study, to show the degree of reprogramming in cloned lambs, we cloned the putative differentially methylated regions (DMRs) of Peg3 from sheep and analyzed the DNA methylation patterns in CpG islands and DMRs of the putative imprinted genes Peg3, Cdkn1c and Gtl2 in cloned lambs. We have provided evidence that Peg3 was highly methylated. The degree of methylation was 95.45% in the kidney and 88.18% in the lung of a natural sheep and 98.18% in the kidney and 87.27% in the lung for one cloned sheep. The bisulphite sequencing results for Cdkn1c show complete non-methylation (0%, 0.53%, 0.53%, 0.53%) in all samples. In addition, Gtl2 was hypomethylated in all lambs, from a linear correlation analysis, there were some differences in the quantitative values from both groups (correlation r² = 0.77). These data show that the DNA methylation status of the three imprinted genes was similar in cloned and natural lambs.