Epigenetic phenomena have been recognized as an important issue in somatic cell nuclear transfer (SCNT) and have been linked to SCNT success rate. We have previously reported a significant maternal lineage effect of oocyte donors on the number of transferable embryos obtained after SCNT (Brüggerhoff et al., 2002 Biol. Reprod. 66, 367–373), pointing to ooplasmic maternal genetic/epigenetic factors important for early embryonic development. We have now extended this study and generated a set of cloned embryos using recipient oocyte pools from defined or random maternal sources that were identified by pedigree data and mitochondrial DNA (mtDNA) haplotype, to study effects of nuclear-cytoplasmic interactions on in utero developmental capacity and fetal phenotype. Embryos were reconstructed from granulosa cells of a Bos taurus (Brown Swiss) cow using oocytes with B. taurus A (Simmental), B. taurus B (Simmental), B. indicus (Dwarf Zebu), or random B. taurus (Brown Swiss) cytoplasm. Two to three embryos per recipient heifer (Simmental) were transferred on Day 7 after SCNT, and fetuses were recovered after slaughter of recipients on Day 80. The number of pregnancies obtained per transferred embryo on Day 28 was similar for the B. taurus combinations (0.11–0.15) but much higher for a limited number of embryos reconstructed with B. indicus cytoplasm (0.50). Developmental capacity of embryos derived from the four oocyte pools varied considerably and resulted in 8 (11.1%), 3 (4.6%), 2 (33%) and 10 (15.2%) viable fetuses with B. taurus A, B. taurus B, B. indicus and random B. taurus cytoplasm, respectively. When fetuses in resorption were included, however, the percentages for recovered fetuses on Day 80 were similar (12.5, 13.8 and 16.7%) in all B. taurus combinations. Body weight, crown rump length, thorax circumference (P < 0.05), and femur length (P < 0.01) of viable fetuses with B. taurus A cytoplasm differed from fetuses with random B. taurus cytoplasm and showed less variation. Furthermore, body weights of fetuses with B. taurus A or B, or B. indicus cytoplasm, were not significantly different from those of B. taurus (Brown Swiss) control fetuses produced by artificial insemination, but fetuses reconstructed with cytoplasts from randomly collected B. taurus oocytes indicated fetal overgrowth (80.6 ± 6.5 g v. 107.9 ± 5.8 g, P < 0.01). Our data point to complex ooplasm-dependent epigenetic modifications and/or nuclear DNA mtDNA interactions that affect developmental capacity and fetal weight and dimensions in SCNT. This might also be relevant for crossbreeding in farm animals and other reproductive technologies such as ooplasmic transfer in human-assisted reproduction