F(1) and backcross hybrids between sexually incompatible species Solanum commersonii and Solanum tuberosum were characterized for glycoalkaloid content and capacity to cold acclimate. Glycoalkaloid (GA) analysis revealed that F(1) triploids and BC(1) pentaploids contained the glycoalkaloids of both parents. In BC(2) (near) tetraploids the situation was different, in that some hybrids produced the GAs of both parents, whereas others contained only the GAs of S. tuberosum. This suggested that the GAs from S. commersonii may be lost rapidly, and that they may have a simple genetic control. The total tuber GA content of BC(1) and BC(2) groups averaged quite acceptable levels (165.9 mg/kg in BC(1) and 192.8 mg/kg in BC(2)), with six genotypes having a GA content <200 mg/kg fresh weight. The F(1) triploid hybrids expressed a capacity to cold acclimate similar to S. commersonii, whereas BC(1) and BC(2) genotypes generally displayed an acclimation capacity higher than the sensitive parent but lower than S. commersonii. However, one BC(1) and two BC(2) genotypes with an acclimation capacity as high as S. commersonii were identified. The polar lipid fatty acid composition in S. commersonii and its hybrid derivatives showed that, following acclimation, there was a significant increase in 18:3. Correlation analysis between the capacity to cold acclimate and the increase in 18:3 was significant, suggesting that the increase in 18:3 can be used as a biochemical marker for the assisted selection of cold-acclimating genotypes in segregating populations.