Pigmentation traits expressed in animals are visual characteristics that allow us to distinguish between breeds and between strains within breed. The objective of this study was to map quantitative trait loci (QTLs) affecting the pigmentation traits in approximately 800 F(2) grand daughter dairy cattle from a Holstein-Friesian and Jersey cross breed cattle. Traits analyzed included pigmentation phenotypes on the body, teat and hoop. The phenoypes were collected from digital photos or visual inspection of live animals. QTL mapping was implemented using half-sib and line-of-descent inheritance models. Our analysis initially detected a number of significant QTLs on chromosomes: 2, 6, 13, 15, 18 and 22. The significant QTLs were divided into two groups: one group influencing the pigmentation color and the other group affecting the absence or level of pigmentation. The most significant QTL peaks were observed on Bovine taurus autosome 18 (BTA18) close to melanocortin 1 receptor (MC1R) for the color traits, on BTA6 close to the receptor tyrosine kinase (KIT) and BTA22 close to microphthalmia-associated transcription factor (MITF) gene for the spotting traits. Association studies were conducted for candidate regions or genes known to affect pigmentation in dairy cattle.