Carotenoids and chlorophylls are among the most widely distributed pigments in nature that play essential roles in the photosynthetic apparatus and confer diverse colours in plants. Among all vegetables, cauliflower (Brassica oleracea L. ssp. var. botrytis) is rich in phytochemicals and is an important crop grown all over the world. This study investigates carotenoid and chlorophyll concentrations in differently pigmented cultivars and elucidates the role of transcriptional regulation of carotenoid accumulation including lutein and β-carotene. Here, we characterised changes in pigments by UHPLC-DAD-ToF-MS and changes in transcript levels of carotenoid metabolic genes by qRT-PCR in florets and leaves of orange (‘Jaffa’ and ‘Sunset’), purple (‘Di Sicilia Violetto’ and ‘Graffiti’), green (‘Trevi’) and white (‘Clapton’) cultivars. Transcript levels of all carotenoid metabolic genes showed different transcript level patterns in the leaves and florets. Compared to the other cultivars, the orange cultivars had the highest levels of β-carotene in the florets and lutein in the leaves resulting in changes lutein/β-carotene ratios. In the green cultivar, higher transcript levels were also found, especially for phytoene synthase and phytoene desaturase genes of the core biosynthesis pathway. However, no increased carotenoid concentrations were observed, possibly due to a higher carotenoid turnover induced by the carotenoid cleavage dioxygenase 4 in the green cultivar. In the white (‘Clapton’) and purple (‘Di Sicilia Violetto’ and ‘Graffiti’) cultivars the phytoene desaturase transcript levels as well as carotenoid concentrations were low. Chlorophyll concentrations changed in trend comparable to the carotenoid concentrations and were only significantly lower in the leaves of the orange cultivar ‘Jaffa’. Also, the chlorophyll a/b ratio changed in ‘Jaffa’. In florets the highest chlorophylls concentrations were observed for the green cultivar (‘Trevi’) and the purple cultivar (‘Di Sicilia Violetto’). Taken together, the study demonstrates the complex source-sink relationship of carotenoid accumulation in different coloured cauliflower.