Most of the above ground tissues in higher plants originate from stem cells located in the shoot apical meristem (SAM). Several plant species suffer from spontaneous stem cell arrest, resulting in lack of further shoot development. In Brassica oleracea this SAM arrest is known as blindness and occurs in an unpredictable manner leading to considerable economic losses for plant raisers and farmers. Detailed analyses of seedlings showed that stem cell arrest is triggered by low temperatures during germination. In this study a comprehensive transcriptome analysis has been performed by RNAseq to identify potential genes underlying cold-induced blindness sensitivity in Brassica oleracea.