The enzyme polyphenol oxidase (PPO) has been implicated in discoloration of Asian noodles. The recombinant inbred line (RIL) populations, M6/'Opata 85', NY18/CC, and ND2603/'Butte 86' were used to investigate the distribution, chromosome location, and number of loci involved in wheat (Triticum aestivum L.) PPO. PPO activity was measured by means of the substrates L-DOPA (L-3,4-dihydroxyphenyl-alanine) and L-tyrosine. The M6/Opata 85 RIL population had a normal distribution, while the ND2603/Butte 86 RIL population had a bimodal distribution for PPO activity (L-DOPA assay). Transgressive segregants were observed for all three populations. Correlations between L-DOPA and L-tyrosine assays for PPO activity were low to medium and could be attributed to substrate specificity and environment. For the combined analysis of M6/Opata 85 RIL populations, the QTL marker Xfba314 (located on chromosome 2D) showed significant association with PPO activity for the L-DOPA assay. For the combined analysis of NY18/CC, three QTL markers for L-DOPA, and two different QTL markers for L-tyrosine, revealed an association with PPO activity at LOD scores of > 2.4. The QTL markers for the NY18/CC RIL population were located on chromosomes 2A, 2B, 3D, and 6B. The ND2603/Butte 86 population had relatively few other loci for linkage analysis and only the marker Xbcd907.RV.I located on chromosome 3BS showed a weak association with PPO activity on the basis of the L-DOPA assay. The identified QTL markers will be useful for marker-assisted selection as they build upon the evolving maps for these populations, and for resolving in greater detail the genetic basis of PPO activity in wheat.