The betalain pigments in ulluco (Ullucus tuberosus), a tuberous crop native to the Andes, have been investigated for the first time using LC-DAD-ESI-MS-MS(2) analyses. Five red, yellow, and red-spotted accessions introduced into New Zealand as a new food crop plus two red tetraploid lines were investigated. Thirty-two different betalains were identified. Both the yellow and red tubers were rich in yellow betaxanthins, and the most prominent among the 20 identified were histidine-betaxanthin, arginine-betaxanthin and glutamine-betaxanthin. Arginine-betaxanthin has been reported to occur naturally only once before and was found in yellow ulluco but not in the red tubers. Twelve betacyanins were found in red tubers, with roughly 50% of this content being betanin/isobetanin. Betacyanin levels were up to 70 microg/g fresh weight in red tubers, but were below quantifiable levels in yellow tubers. Betaxanthin levels were up to 50 microg/g fresh weight in yellow tubers. Interference by betacyanins in measuring levels of betaxanthins by visible spectrophotometry is discussed. Low concentrations of betalains were detected in leaves, whereas stems contained total levels similar to the tubers, with dopamine-betaxanthin and betanin being the major pigments. This is the first report describing both the betacyanin and betaxanthin patterns in a plant from the Basellaceae family.