Head and neck squamous cell carcinoma (HNSCC) is a global public health problem, which increases in prevalence every year. Evidence brings up that small populations of stem cells, the cancer stem cells (CSC), are responsible for tumour initiation, tumorigenesis, progression, and metastasis. These cells play a crucial role in cancer development and treatment response, but the origin of CSCs remains unclear. In this research, we have sequenced the entire exome of the three different groups of cells of primary squamous cell carcinoma tumour from different patients, with the aim to understand their main genetic changes and to elucidate the possible origin of tumour cells and tumour stem cells.We performed a whole exome sequencing in the germinal line, tumour cells, and CSC ALDH+ samples from four HNSCC patients. An analysis pipeline was used to filter, score, rank, and prioritize candidate variants according to its effect on protein structure and phylogenetic conservation using available information on pathways and protein function databases.Results showed variations in genes involved in oncogenic pathways and shed light on the evolution model of the CSC and tumour cells for each patient in which stem cells (CS) triggered the formation of CSC and these in turn become tumour cells.These findings support the idea that it is possible to identify in each individual patient if the CS are of tumour origin or vice versa, thus being possible a more personalized treatment.